@gmod/bbi 5.0.1 → 6.0.0

package/dist/block-view.js

@@ -1,25 +1,16 @@
 "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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BlockView = void 0;
-const buffer_1 = require("buffer");
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 // locals
 const range_1 = __importDefault(require("./range"));
 const unzip_1 = require("./unzip");
 const util_1 = require("./util");
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function coordFilter(s1, e1, s2, e2) {
     return s1 < e2 && e1 >= s2;
 }
@@ -31,180 +22,178 @@ function coordFilter(s1, e1, s2, e2) {
  * @constructs
  */
 class BlockView {
-    constructor(bbi, refsByName, cirTreeOffset, isBigEndian, isCompressed, blockType) {
+    constructor(bbi, refsByName, cirTreeOffset, isCompressed, blockType) {
         this.bbi = bbi;
         this.refsByName = refsByName;
         this.cirTreeOffset = cirTreeOffset;
-        this.isBigEndian = isBigEndian;
         this.isCompressed = isCompressed;
         this.blockType = blockType;
         this.featureCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1000 }),
-            fill: (requestData, signal) => __awaiter(this, void 0, void 0, function* () {
-                const len = requestData.length;
-                const off = requestData.offset;
-                const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(len), 0, len, off, {
+            fill: async (requestData, signal) => {
+                return this.bbi.read(requestData.length, requestData.offset, {
                     signal,
                 });
-                return buffer;
-            }),
+            },
         });
         if (!(cirTreeOffset >= 0)) {
             throw new Error('invalid cirTreeOffset!');
         }
     }
-    readWigData(chrName, start, end, observer, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            try {
-                const { refsByName, bbi, cirTreeOffset, isBigEndian } = this;
-                const chrId = refsByName[chrName];
-                if (chrId === undefined) {
-                    observer.complete();
-                }
-                const request = { chrId, start, end };
-                if (!this.cirTreePromise) {
-                    this.cirTreePromise = bbi.read(buffer_1.Buffer.alloc(48), 0, 48, cirTreeOffset, opts);
-                }
-                const { buffer } = yield this.cirTreePromise;
-                const cirBlockSize = isBigEndian
-                    ? buffer.readUInt32BE(4)
-                    : buffer.readUInt32LE(4);
-                let blocksToFetch = [];
-                let outstanding = 0;
-                const le = true;
-                const cirFobRecur2 = (cirBlockData, offset2, level) => {
-                    try {
-                        const data = cirBlockData.subarray(offset2);
-                        const b = data;
-                        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-                        let offset = 0;
-                        const isLeaf = dataView.getUint8(offset);
-                        offset += 2; // 1 skip
-                        const cnt = dataView.getUint16(offset, le);
-                        offset += 2;
-                        if (isLeaf === 1) {
-                            const blocksToFetch2 = [];
-                            for (let i = 0; i < cnt; i++) {
-                                const startChrom = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const startBase = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const endChrom = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const endBase = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const blockOffset = Number(dataView.getBigUint64(offset, le));
-                                offset += 8;
-                                const blockSize = Number(dataView.getBigUint64(offset, le));
-                                offset += 8;
-                                blocksToFetch2.push({
-                                    startChrom,
-                                    startBase,
-                                    endBase,
-                                    endChrom,
-                                    blockOffset,
-                                    blockSize,
-                                    offset,
-                                });
-                            }
-                            blocksToFetch = blocksToFetch.concat(blocksToFetch2
-                                .filter(f => filterFeats(f))
-                                .map(l => ({
-                                offset: l.blockOffset,
-                                length: l.blockSize,
-                            })));
-                        }
-                        else if (isLeaf === 0) {
-                            const recurOffsets = [];
-                            for (let i = 0; i < cnt; i++) {
-                                const startChrom = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const startBase = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const endChrom = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const endBase = dataView.getUint32(offset, le);
-                                offset += 4;
-                                const blockOffset = Number(dataView.getBigUint64(offset, le));
-                                offset += 8;
-                                recurOffsets.push({
-                                    startChrom,
-                                    startBase,
-                                    endChrom,
-                                    endBase,
-                                    blockOffset,
-                                    offset,
-                                });
-                            }
-                            const recurOffsets2 = recurOffsets
-                                .filter(f => filterFeats(f))
-                                .map(l => l.blockOffset);
-                            if (recurOffsets2.length > 0) {
-                                cirFobRecur(recurOffsets2, level + 1);
-                            }
+    async readWigData(chrName, start, end, observer, opts) {
+        try {
+            const { refsByName, bbi, cirTreeOffset } = this;
+            const chrId = refsByName[chrName];
+            if (chrId === undefined) {
+                observer.complete();
+            }
+            const request = { chrId, start, end };
+            if (!this.cirTreePromise) {
+                this.cirTreePromise = bbi.read(48, cirTreeOffset, opts);
+            }
+            const buffer = await this.cirTreePromise;
+            const dataView = new DataView(buffer.buffer);
+            const cirBlockSize = dataView.getUint32(4, true);
+            let blocksToFetch = [];
+            let outstanding = 0;
+            const cirFobRecur2 = (cirBlockData, offset2, level) => {
+                try {
+                    const data = cirBlockData.subarray(offset2);
+                    const b = data;
+                    const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+                    let offset = 0;
+                    const isLeaf = dataView.getUint8(offset);
+                    offset += 2; // 1 skip
+                    const cnt = dataView.getUint16(offset, true);
+                    offset += 2;
+                    if (isLeaf === 1) {
+                        const blocksToFetch2 = [];
+                        for (let i = 0; i < cnt; i++) {
+                            const startChrom = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const startBase = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const endChrom = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const endBase = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const blockOffset = Number(dataView.getBigUint64(offset, true));
+                            offset += 8;
+                            const blockSize = Number(dataView.getBigUint64(offset, true));
+                            offset += 8;
+                            blocksToFetch2.push({
+                                startChrom,
+                                startBase,
+                                endBase,
+                                endChrom,
+                                blockOffset,
+                                blockSize,
+                                offset,
+                            });
                         }
+                        blocksToFetch = blocksToFetch.concat(blocksToFetch2
+                            .filter(f => filterFeats(f))
+                            .map(l => ({
+                            offset: l.blockOffset,
+                            length: l.blockSize,
+                        })));
                     }
-                    catch (e) {
-                        observer.error(e);
+                    else if (isLeaf === 0) {
+                        const recurOffsets = [];
+                        for (let i = 0; i < cnt; i++) {
+                            const startChrom = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const startBase = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const endChrom = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const endBase = dataView.getUint32(offset, true);
+                            offset += 4;
+                            const blockOffset = Number(dataView.getBigUint64(offset, true));
+                            offset += 8;
+                            recurOffsets.push({
+                                startChrom,
+                                startBase,
+                                endChrom,
+                                endBase,
+                                blockOffset,
+                                offset,
+                            });
+                        }
+                        const recurOffsets2 = recurOffsets
+                            .filter(f => filterFeats(f))
+                            .map(l => l.blockOffset);
+                        if (recurOffsets2.length > 0) {
+                            cirFobRecur(recurOffsets2, level + 1);
+                        }
                     }
-                };
-                const filterFeats = (b) => {
-                    const { startChrom, startBase, endChrom, endBase } = b;
-                    return ((startChrom < chrId || (startChrom === chrId && startBase <= end)) &&
-                        (endChrom > chrId || (endChrom === chrId && endBase >= start)));
-                };
-                const cirFobStartFetch = (off, fr, level) => __awaiter(this, void 0, void 0, function* () {
-                    try {
-                        const length = fr.max - fr.min;
-                        const offset = fr.min;
-                        const resultBuffer = yield this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
-                        for (const element of off) {
-                            if (fr.contains(element)) {
-                                cirFobRecur2(resultBuffer, element - offset, level);
-                                outstanding -= 1;
-                                if (outstanding === 0) {
-                                    this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request })).catch(e => observer.error(e));
-                                }
+                }
+                catch (e) {
+                    observer.error(e);
+                }
+            };
+            const filterFeats = (b) => {
+                const { startChrom, startBase, endChrom, endBase } = b;
+                return ((startChrom < chrId || (startChrom === chrId && startBase <= end)) &&
+                    (endChrom > chrId || (endChrom === chrId && endBase >= start)));
+            };
+            const cirFobStartFetch = async (off, fr, level) => {
+                try {
+                    const length = fr.max - fr.min;
+                    const offset = fr.min;
+                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts?.signal);
+                    for (const element of off) {
+                        if (fr.contains(element)) {
+                            cirFobRecur2(resultBuffer, element - offset, level);
+                            outstanding -= 1;
+                            if (outstanding === 0) {
+                                this.readFeatures(observer, blocksToFetch, {
+                                    ...opts,
+                                    request,
+                                }).catch((e) => {
+                                    observer.error(e);
+                                });
                             }
                         }
                     }
-                    catch (e) {
-                        observer.error(e);
-                    }
-                });
-                const cirFobRecur = (offset, level) => {
-                    try {
-                        outstanding += offset.length;
-                        // Upper bound on size, based on a completely full leaf node.
-                        const maxCirBlockSpan = 4 + cirBlockSize * 32;
-                        let spans = new range_1.default([
+                }
+                catch (e) {
+                    observer.error(e);
+                }
+            };
+            const cirFobRecur = (offset, level) => {
+                try {
+                    outstanding += offset.length;
+                    // Upper bound on size, based on a completely full leaf node.
+                    const maxCirBlockSpan = 4 + cirBlockSize * 32;
+                    let spans = new range_1.default([
+                        {
+                            min: offset[0],
+                            max: offset[0] + maxCirBlockSpan,
+                        },
+                    ]);
+                    for (let i = 1; i < offset.length; i += 1) {
+                        const blockSpan = new range_1.default([
                             {
-                                min: offset[0],
-                                max: offset[0] + maxCirBlockSpan,
+                                min: offset[i],
+                                max: offset[i] + maxCirBlockSpan,
                             },
                         ]);
-                        for (let i = 1; i < offset.length; i += 1) {
-                            const blockSpan = new range_1.default([
-                                {
-                                    min: offset[i],
-                                    max: offset[i] + maxCirBlockSpan,
-                                },
-                            ]);
-                            spans = spans.union(blockSpan);
-                        }
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                        spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
-                    }
-                    catch (e) {
-                        observer.error(e);
+                        spans = spans.union(blockSpan);
                     }
-                };
-                return cirFobRecur([Number(cirTreeOffset) + 48], 1);
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        });
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
+                }
+                catch (e) {
+                    observer.error(e);
+                }
+            };
+            cirFobRecur([Number(cirTreeOffset) + 48], 1);
+            return;
+        }
+        catch (e) {
+            observer.error(e);
+        }
     }
     parseSummaryBlock(b, startOffset, request) {
         const features = [];
@@ -249,16 +238,15 @@ class BlockView {
     parseBigBedBlock(data, startOffset, offset, request) {
         const items = [];
         let currOffset = startOffset;
-        const le = true;
         const b = data;
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         while (currOffset < data.byteLength) {
             const c2 = currOffset;
-            const chromId = dataView.getUint32(currOffset, le);
+            const chromId = dataView.getUint32(currOffset, true);
             currOffset += 4;
-            const start = dataView.getInt32(currOffset, le);
+            const start = dataView.getInt32(currOffset, true);
             currOffset += 4;
-            const end = dataView.getInt32(currOffset, le);
+            const end = dataView.getInt32(currOffset, true);
             currOffset += 4;
             let i = currOffset;
             for (; i < data.length; i++) {
@@ -266,7 +254,8 @@ class BlockView {
                     break;
                 }
             }
-            const rest = data.subarray(currOffset, i).toString();
+            const b = data.subarray(currOffset, i);
+            const rest = decoder?.decode(b) ?? b.toString();
             currOffset = i + 1;
             items.push({
                 chromId,
@@ -345,51 +334,47 @@ class BlockView {
             ? items.filter(f => coordFilter(f.start, f.end, req.start, req.end))
             : items;
     }
-    readFeatures(observer_1, blocks_1) {
-        return __awaiter(this, arguments, void 0, function* (observer, blocks, opts = {}) {
-            try {
-                const { blockType, isCompressed } = this;
-                const { signal, request } = opts;
-                const blockGroupsToFetch = (0, util_1.groupBlocks)(blocks);
+    async readFeatures(observer, blocks, opts = {}) {
+        try {
+            const { blockType, isCompressed } = this;
+            const { signal, request } = opts;
+            const blockGroupsToFetch = (0, util_1.groupBlocks)(blocks);
+            (0, util_1.checkAbortSignal)(signal);
+            await Promise.all(blockGroupsToFetch.map(async (blockGroup) => {
                 (0, util_1.checkAbortSignal)(signal);
-                yield Promise.all(blockGroupsToFetch.map((blockGroup) => __awaiter(this, void 0, void 0, function* () {
+                const { length, offset } = blockGroup;
+                const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
+                for (const block of blockGroup.blocks) {
+                    (0, util_1.checkAbortSignal)(signal);
+                    let resultData = data.subarray(Number(block.offset) - Number(blockGroup.offset));
+                    if (isCompressed) {
+                        resultData = (0, unzip_1.unzip)(resultData);
+                    }
                     (0, util_1.checkAbortSignal)(signal);
-                    const { length, offset } = blockGroup;
-                    const data = yield this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
-                    for (const block of blockGroup.blocks) {
-                        (0, util_1.checkAbortSignal)(signal);
-                        let blockOffset = Number(block.offset) - Number(blockGroup.offset);
-                        let resultData = data;
-                        if (isCompressed) {
-                            resultData = (0, unzip_1.unzip)(data.subarray(blockOffset));
-                            blockOffset = 0;
+                    switch (blockType) {
+                        case 'summary': {
+                            observer.next(this.parseSummaryBlock(resultData, 0, request));
+                            break;
                         }
-                        (0, util_1.checkAbortSignal)(signal);
-                        switch (blockType) {
-                            case 'summary': {
-                                observer.next(this.parseSummaryBlock(resultData, blockOffset, request));
-                                break;
-                            }
-                            case 'bigwig': {
-                                observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
-                                break;
-                            }
-                            case 'bigbed': {
-                                observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
-                                break;
-                            }
-                            default: {
-                                console.warn(`Don't know what to do with ${blockType}`);
-                            }
+                        case 'bigwig': {
+                            observer.next(this.parseBigWigBlock(resultData, 0, request));
+                            break;
+                        }
+                        case 'bigbed': {
+                            observer.next(this.parseBigBedBlock(resultData, 0, Number(block.offset) * (1 << 8), request));
+                            break;
+                        }
+                        default: {
+                            console.warn(`Don't know what to do with ${blockType}`);
                         }
                     }
-                })));
-                observer.complete();
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        });
+                }
+            }));
+            observer.complete();
+        }
+        catch (e) {
+            observer.error(e);
+        }
     }
 }
 exports.BlockView = BlockView;

package/dist/block-view.js.map

@@ -1 +1 @@
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package/dist/unzip-pako.d.ts

@@ -1,2 +1 @@
-import { Buffer } from 'buffer';
-export declare function unzip(input: Buffer): Uint8Array;
+export declare function unzip(input: Uint8Array): Uint8Array;

package/dist/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;AAGA,sBAEC;AAJD,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;AAEA,sBAEC;AAJD,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAiB;IACrC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}

package/dist/util.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.AbortError = void 0;
 exports.groupBlocks = groupBlocks;
@@ -75,10 +66,8 @@ function checkAbortSignal(signal) {
  * provide a place to break when an abort signal is received.
  * @param {AbortSignal} signal
  */
-function abortBreakPoint(signal) {
-    return __awaiter(this, void 0, void 0, function* () {
-        yield Promise.resolve();
-        checkAbortSignal(signal);
-    });
+async function abortBreakPoint(signal) {
+    await Promise.resolve();
+    checkAbortSignal(signal);
 }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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