@gmod/bbi 5.0.2 → 6.0.0

package/dist/bigbed.js

@@ -1,31 +1,10 @@
 "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());
-    });
-};
-var __rest = (this && this.__rest) || function (s, e) {
-    var t = {};
-    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
-        t[p] = s[p];
-    if (s != null && typeof Object.getOwnPropertySymbols === "function")
-        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
-            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
-                t[p[i]] = s[p[i]];
-        }
-    return t;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = void 0;
 exports.filterUndef = filterUndef;
-const buffer_1 = require("buffer");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
@@ -40,20 +19,18 @@ class BigBed extends bbi_1.BBI {
         super(...arguments);
         this.readIndicesCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (args, signal) => this._readIndices(Object.assign(Object.assign({}, args), { signal })),
+            fill: (args, signal) => this._readIndices({ ...args, signal }),
         });
     }
     readIndices(opts = {}) {
-        const { signal } = opts, rest = __rest(opts, ["signal"]);
+        const { signal, ...rest } = opts;
         return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
     }
     /*
      * retrieve unzoomed view for any scale
      */
-    getView(_scale, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.getUnzoomedView(opts);
-        });
+    async getView(_scale, opts) {
+        return this.getUnzoomedView(opts);
     }
     /*
      * parse the bigbed extraIndex fields
@@ -62,137 +39,137 @@ class BigBed extends bbi_1.BBI {
      * @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;
-            const b = data;
+    async _readIndices(opts) {
+        const { extHeaderOffset } = await this.getHeader(opts);
+        const b = await this.bbi.read(64, Number(extHeaderOffset));
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        // const _size = dataView.getUint16(offset, true)
+        offset += 2;
+        const count = dataView.getUint16(offset, true);
+        offset += 2;
+        const dataOffset = Number(dataView.getBigUint64(offset, true));
+        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(len, Number(dataOffset));
+        const indices = [];
+        for (let i = 0; i < count; i += 1) {
+            const b = buffer.subarray(i * blocklen);
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
             let offset = 0;
-            // const _size = dataView.getUint16(offset, le)
+            const type = dataView.getInt16(offset, true);
             offset += 2;
-            const count = dataView.getUint16(offset, le);
+            const fieldcount = dataView.getInt16(offset, true);
             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(dataOffset));
-            const indices = [];
-            for (let i = 0; i < count; i += 1) {
-                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;
-        });
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
+            offset += 8 + 4; //4 skip
+            const field = dataView.getInt16(offset, true);
+            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
      *
      * @param name - the name to search for
+     *
      * @param opts - a SearchOptions argument with optional signal
+     *
      * @return a Promise for an array of bigbed block Loc entries
      */
-    searchExtraIndexBlocks(name_1) {
-        return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
-            const { isBigEndian } = yield this.getHeader(opts);
-            const indices = yield this.readIndices(opts);
-            if (indices.length === 0) {
-                return [];
-            }
-            const locs = indices.map((index) => __awaiter(this, void 0, void 0, function* () {
-                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;
+    async searchExtraIndexBlocks(name, opts = {}) {
+        const indices = await this.readIndices(opts);
+        if (indices.length === 0) {
+            return [];
+        }
+        const decoder = new TextDecoder('utf8');
+        const locs = indices.map(async (index) => {
+            const { offset: offset2, field } = index;
+            const b = await this.bbi.read(32, offset2, opts);
+            const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            let offset = 0;
+            // const _magic = dataView.getInt32(offset, true)
+            offset += 4;
+            const blockSize = dataView.getInt32(offset, true);
+            offset += 4;
+            const keySize = dataView.getInt32(offset, true);
+            offset += 4;
+            const valSize = dataView.getInt32(offset, true);
+            offset += 4;
+            // const _itemCount = Number(dataView.getBigUint64(offset, true))
+            offset += 8;
+            const bptReadNode = async (nodeOffset) => {
+                const val = Number(nodeOffset);
+                const len = 4 + blockSize * (keySize + valSize);
+                const buffer = await this.bbi.read(len, val, opts);
+                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 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 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);
-                            }
-                            lastOffset = offset;
-                        }
-                        return bptReadNode(lastOffset);
+                const nodeType = dataView.getInt8(offset);
+                offset += 2; //skip 1
+                const cnt = dataView.getInt16(offset, true);
+                offset += 2;
+                const keys = [];
+                if (nodeType === 0) {
+                    const leafkeys = [];
+                    for (let i = 0; i < cnt; i++) {
+                        const key = decoder
+                            .decode(b.subarray(offset, offset + keySize))
+                            .replaceAll('\0', '');
+                        offset += keySize;
+                        const dataOffset = Number(dataView.getBigUint64(offset, true));
+                        offset += 8;
+                        leafkeys.push({
+                            key,
+                            offset: dataOffset,
+                        });
                     }
-                    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 });
+                    let lastOffset = 0;
+                    for (const { key, offset } of leafkeys) {
+                        if (name.localeCompare(key) < 0 && lastOffset) {
+                            return bptReadNode(lastOffset);
                         }
-                        for (const n of keys) {
-                            if (n.key === name) {
-                                return Object.assign(Object.assign({}, n), { field });
-                            }
+                        lastOffset = offset;
+                    }
+                    return bptReadNode(lastOffset);
+                }
+                else if (nodeType === 1) {
+                    for (let i = 0; i < cnt; i++) {
+                        const key = decoder
+                            .decode(b.subarray(offset, offset + keySize))
+                            .replaceAll('\0', '');
+                        offset += keySize;
+                        const dataOffset = Number(dataView.getBigUint64(offset, true));
+                        offset += 8;
+                        const length = dataView.getUint32(offset, true);
+                        offset += 4;
+                        const reserved = dataView.getUint32(offset, true);
+                        offset += 4;
+                        keys.push({
+                            key,
+                            offset: dataOffset,
+                            length,
+                            reserved,
+                        });
+                    }
+                    for (const n of keys) {
+                        if (n.key === name) {
+                            return { ...n, field };
                         }
-                        return undefined;
                     }
-                });
-                const rootNodeOffset = 32;
-                return bptReadNode(offset2 + rootNodeOffset);
-            }));
-            return filterUndef(yield Promise.all(locs));
+                    return undefined;
+                }
+            };
+            const rootNodeOffset = 32;
+            return bptReadNode(offset2 + rootNodeOffset);
         });
+        return filterUndef(await Promise.all(locs));
     }
     /*
      * retrieve the features from the bigbed data that were found through the
@@ -200,31 +177,31 @@ class BigBed extends bbi_1.BBI {
      * the BigBed specification and the -extraIndex argument to bedToBigBed
      *
      * @param name - the name to search for
-     * @param opts - a SearchOptions argument with optional signal
-     * @return a Promise for an array of Feature
+     *
+     * @param opts - options object with optional AboutSignal
+     *
+     * @return array of Feature
      */
-    searchExtraIndex(name_1) {
-        return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
-            const blocks = yield this.searchExtraIndexBlocks(name, opts);
-            if (blocks.length === 0) {
-                return [];
-            }
-            const view = yield this.getUnzoomedView(opts);
-            const res = blocks.map(block => {
-                return new rxjs_1.Observable(observer => {
-                    view.readFeatures(observer, [block], opts).catch((e) => {
-                        observer.error(e);
-                    });
-                }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
-                    for (const element of x) {
-                        element.field = block.field;
-                    }
-                    return x;
-                }));
-            });
-            const ret = yield (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
-            return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
+    async searchExtraIndex(name, opts = {}) {
+        const blocks = await this.searchExtraIndexBlocks(name, opts);
+        if (blocks.length === 0) {
+            return [];
+        }
+        const view = await this.getUnzoomedView(opts);
+        const res = blocks.map(block => {
+            return new rxjs_1.Observable(observer => {
+                view.readFeatures(observer, [block], opts).catch((e) => {
+                    observer.error(e);
+                });
+            }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
+                for (const element of x) {
+                    element.field = block.field;
+                }
+                return x;
+            }));
         });
+        const ret = await (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
+        return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name);
     }
 }
 exports.BigBed = BigBed;

package/dist/bigbed.js.map

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

@@ -1,13 +1,4 @@
 "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.BigWig = void 0;
 const block_view_1 = require("./block-view");
@@ -21,20 +12,18 @@ class BigWig extends bbi_1.BBI {
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
      * or scale used to infer the zoomLevel to use
      */
-    getView(scale, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { zoomLevels, refsByName, isBigEndian, uncompressBufSize } = yield this.getHeader(opts);
-            const basesPerPx = 1 / scale;
-            const maxLevel = zoomLevels.length - 1;
-            for (let i = maxLevel; i >= 0; i -= 1) {
-                const zh = zoomLevels[i];
-                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                    return new block_view_1.BlockView(this.bbi, refsByName, zh.indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
-                }
+    async getView(scale, opts) {
+        const { zoomLevels, refsByName, uncompressBufSize } = await this.getHeader(opts);
+        const basesPerPx = 1 / scale;
+        const maxLevel = zoomLevels.length - 1;
+        for (let i = maxLevel; i >= 0; i -= 1) {
+            const zh = zoomLevels[i];
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            if (zh && zh.reductionLevel <= 2 * basesPerPx) {
+                return new block_view_1.BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize > 0, 'summary');
             }
-            return this.getUnzoomedView(opts);
-        });
+        }
+        return this.getUnzoomedView(opts);
     }
 }
 exports.BigWig = BigWig;

package/dist/bigwig.js.map

@@ -1 +1 @@
-{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;;;OAOG;IACa,OAAO,CAAC,KAAa,EAAE,IAAoB;;YACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAC9D,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;YAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;YAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBACxB,uEAAuE;gBACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;oBAC9C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;YACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;CACF;AA/BD,wBA+BC"}
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF;AA9BD,wBA8BC"}

package/dist/block-view.d.ts

@@ -1,5 +1,5 @@
 import { Observer } from 'rxjs';
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import { Feature } from './bbi';
 interface CoordRequest {
     chrId: number;
@@ -21,12 +21,11 @@ export declare class BlockView {
     private bbi;
     private refsByName;
     private cirTreeOffset;
-    private isBigEndian;
     private isCompressed;
     private blockType;
     private cirTreePromise?;
     private featureCache;
-    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
+    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isCompressed: boolean, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;