@gmod/bbi 1.0.35 → 2.0.0

package/esm/blockView.js

@@ -1,12 +1,16 @@
-import { Parser } from '@gmod/binary-parser';
+import { Parser } from 'binary-parser';
 import AbortablePromiseCache from 'abortable-promise-cache';
-import { unzip } from './unzip';
 import QuickLRU from 'quick-lru';
+// locals
 import Range from './range';
+import { unzip } from './unzip';
 import { groupBlocks, checkAbortSignal } from './util';
 const BIG_WIG_TYPE_GRAPH = 1;
 const BIG_WIG_TYPE_VSTEP = 2;
 const BIG_WIG_TYPE_FSTEP = 3;
+function coordFilter(s1, e1, s2, e2) {
+    return s1 < e2 && e1 >= s2;
+}
 function getParsers(isBigEndian) {
     const le = isBigEndian ? 'big' : 'little';
     const summaryParser = new Parser()
@@ -15,10 +19,11 @@ function getParsers(isBigEndian) {
         .uint32('start')
         .uint32('end')
         .uint32('validCnt')
-        .float('minScore')
-        .float('maxScore')
-        .float('sumData')
-        .float('sumSqData');
+        .floatle('minScore')
+        .floatle('maxScore')
+        .floatle('sumData')
+        .floatle('sumSqData')
+        .saveOffset('offset');
     const leafParser = new Parser()
         .endianess(le)
         .uint8('isLeaf')
@@ -27,24 +32,28 @@ function getParsers(isBigEndian) {
         .choice({
         tag: 'isLeaf',
         choices: {
-            1: new Parser().array('blocksToFetch', {
+            1: new Parser().endianess(le).array('blocksToFetch', {
                 length: 'cnt',
                 type: new Parser()
+                    .endianess(le)
                     .uint32('startChrom')
                     .uint32('startBase')
                     .uint32('endChrom')
                     .uint32('endBase')
                     .uint64('blockOffset')
-                    .uint64('blockSize'),
+                    .uint64('blockSize')
+                    .saveOffset('offset'),
             }),
             0: new Parser().array('recurOffsets', {
                 length: 'cnt',
                 type: new Parser()
+                    .endianess(le)
                     .uint32('startChrom')
                     .uint32('startBase')
                     .uint32('endChrom')
                     .uint32('endBase')
-                    .uint64('blockOffset'),
+                    .uint64('blockOffset')
+                    .saveOffset('offset'),
             }),
         },
     });
@@ -55,7 +64,8 @@ function getParsers(isBigEndian) {
         .int32('end')
         .string('rest', {
         zeroTerminated: true,
-    });
+    })
+        .saveOffset('offset');
     const bigWigParser = new Parser()
         .endianess(le)
         .skip(4)
@@ -71,15 +81,19 @@ function getParsers(isBigEndian) {
         choices: {
             [BIG_WIG_TYPE_FSTEP]: new Parser().array('items', {
                 length: 'itemCount',
-                type: new Parser().float('score'),
+                type: new Parser().floatle('score'),
             }),
             [BIG_WIG_TYPE_VSTEP]: new Parser().array('items', {
                 length: 'itemCount',
-                type: new Parser().int32('start').float('score'),
+                type: new Parser().endianess(le).int32('start').floatle('score'),
             }),
             [BIG_WIG_TYPE_GRAPH]: new Parser().array('items', {
                 length: 'itemCount',
-                type: new Parser().int32('start').int32('end').float('score'),
+                type: new Parser()
+                    .endianess(le)
+                    .int32('start')
+                    .int32('end')
+                    .floatle('score'),
             }),
         },
     });
@@ -98,43 +112,42 @@ function getParsers(isBigEndian) {
  * @constructs
  */
 export class BlockView {
-    constructor(bbi, refsByName, cirTreeOffset, cirTreeLength, isBigEndian, isCompressed, blockType) {
+    constructor(bbi, refsByName, cirTreeOffset, isBigEndian, isCompressed, blockType) {
+        this.bbi = bbi;
+        this.refsByName = refsByName;
+        this.cirTreeOffset = cirTreeOffset;
+        this.isBigEndian = isBigEndian;
+        this.isCompressed = isCompressed;
+        this.blockType = blockType;
         this.featureCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1000 }),
             fill: async (requestData, signal) => {
-                const { length, offset } = requestData;
-                const { buffer } = await this.bbi.read(Buffer.alloc(length), 0, length, offset, { signal });
+                const len = Number(requestData.length);
+                const off = Number(requestData.offset);
+                const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, off, {
+                    signal,
+                });
                 return buffer;
             },
         });
         if (!(cirTreeOffset >= 0)) {
             throw new Error('invalid cirTreeOffset!');
         }
-        if (!(cirTreeLength > 0)) {
-            throw new Error('invalid cirTreeLength!');
-        }
-        this.cirTreeOffset = cirTreeOffset;
-        this.cirTreeLength = cirTreeLength;
-        this.isCompressed = isCompressed;
-        this.refsByName = refsByName;
-        this.isBigEndian = isBigEndian;
-        this.bbi = bbi;
-        this.blockType = blockType;
-        Object.assign(this, getParsers(isBigEndian));
+        const parsers = getParsers(isBigEndian);
+        this.leafParser = parsers.leafParser;
+        this.bigBedParser = parsers.bigBedParser;
     }
     async readWigData(chrName, start, end, observer, opts) {
         try {
             const { refsByName, bbi, cirTreeOffset, isBigEndian } = this;
-            const { signal } = opts;
             const chrId = refsByName[chrName];
             if (chrId === undefined) {
                 observer.complete();
             }
             const request = { chrId, start, end };
             if (!this.cirTreePromise) {
-                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, cirTreeOffset, {
-                    signal,
-                });
+                const off = Number(cirTreeOffset);
+                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, off, opts);
             }
             const { buffer } = await this.cirTreePromise;
             const cirBlockSize = isBigEndian
@@ -144,10 +157,12 @@ export class BlockView {
             let outstanding = 0;
             const cirFobRecur2 = (cirBlockData, offset, level) => {
                 try {
-                    const data = cirBlockData.slice(offset);
-                    const p = this.leafParser.parse(data).result;
+                    const data = cirBlockData.subarray(offset);
+                    const p = this.leafParser.parse(data);
                     if (p.blocksToFetch) {
-                        blocksToFetch = blocksToFetch.concat(p.blocksToFetch.filter(filterFeats).map((l) => ({
+                        blocksToFetch = blocksToFetch.concat(p.blocksToFetch
+                            .filter(filterFeats)
+                            .map((l) => ({
                             offset: l.blockOffset,
                             length: l.blockSize,
                         })));
@@ -155,7 +170,7 @@ export class BlockView {
                     if (p.recurOffsets) {
                         const recurOffsets = p.recurOffsets
                             .filter(filterFeats)
-                            .map((l) => l.blockOffset);
+                            .map((l) => Number(l.blockOffset));
                         if (recurOffsets.length > 0) {
                             cirFobRecur(recurOffsets, level + 1);
                         }
@@ -174,7 +189,7 @@ export class BlockView {
                 try {
                     const length = fr.max() - fr.min();
                     const offset = fr.min();
-                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, signal);
+                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts.signal);
                     for (let i = 0; i < off.length; i += 1) {
                         if (fr.contains(off[i])) {
                             cirFobRecur2(resultBuffer, off[i] - offset, level);
@@ -192,7 +207,7 @@ export class BlockView {
             const cirFobRecur = (offset, level) => {
                 try {
                     outstanding += offset.length;
-                    const maxCirBlockSpan = 4 + cirBlockSize * 32; // Upper bound on size, based on a completely full leaf node.
+                    const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32; // Upper bound on size, based on a completely full leaf node.
                     let spans = new Range(offset[0], offset[0] + maxCirBlockSpan);
                     for (let i = 1; i < offset.length; i += 1) {
                         const blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan);
@@ -204,71 +219,114 @@ export class BlockView {
                     observer.error(e);
                 }
             };
-            return cirFobRecur([cirTreeOffset + 48], 1);
+            return cirFobRecur([Number(cirTreeOffset) + 48], 1);
         }
         catch (e) {
             observer.error(e);
         }
     }
-    parseSummaryBlock(data, startOffset, request) {
+    parseSummaryBlock(buffer, startOffset, request) {
         const features = [];
-        let currOffset = startOffset;
-        while (currOffset < data.byteLength) {
-            const res = this.summaryParser.parse(data.slice(currOffset));
-            features.push(res.result);
-            currOffset += res.offset;
-        }
-        let items = features;
-        if (request) {
-            items = items.filter(elt => elt.chromId === request.chrId);
+        let offset = startOffset;
+        const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+        while (offset < buffer.byteLength) {
+            // this was extracted from looking at the runtime code generated by
+            // binary-parser
+            const chromId = dataView.getUint32(offset, true);
+            offset += 4;
+            const start = dataView.getUint32(offset, true);
+            offset += 4;
+            const end = dataView.getUint32(offset, true);
+            offset += 4;
+            const validCnt = dataView.getUint32(offset, true);
+            offset += 4;
+            const minScore = dataView.getFloat32(offset, true);
+            offset += 4;
+            const maxScore = dataView.getFloat32(offset, true);
+            offset += 4;
+            const sumData = dataView.getFloat32(offset, true);
+            offset += 4;
+            // unused
+            // const sumSqData = dataView.getFloat32(offset, true)
+            offset += 4;
+            if (request
+                ? chromId === request.chrId &&
+                    coordFilter(start, end, request.start, request.end)
+                : true) {
+                features.push({
+                    start,
+                    end,
+                    maxScore,
+                    minScore,
+                    summary: true,
+                    score: sumData / (validCnt || 1),
+                });
+            }
         }
-        const feats = items.map((elt) => ({
-            start: elt.start,
-            end: elt.end,
-            maxScore: elt.maxScore,
-            minScore: elt.minScore,
-            score: elt.sumData / (elt.validCnt || 1),
-            summary: true,
-        }));
-        return request
-            ? feats.filter(f => BlockView.coordFilter(f, request))
-            : feats;
+        return features;
     }
     parseBigBedBlock(data, startOffset, offset, request) {
         const items = [];
         let currOffset = startOffset;
         while (currOffset < data.byteLength) {
-            const res = this.bigBedParser.parse(data.slice(currOffset));
-            res.result.uniqueId = `bb-${offset + currOffset}`;
-            items.push(res.result);
+            const res = this.bigBedParser.parse(data.subarray(currOffset));
+            items.push({ ...res, uniqueId: `bb-${offset + currOffset}` });
             currOffset += res.offset;
         }
         return request
-            ? items.filter((f) => BlockView.coordFilter(f, request))
+            ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
             : items;
     }
-    parseBigWigBlock(bytes, startOffset, request) {
-        const data = bytes.slice(startOffset);
-        const results = this.bigWigParser.parse(data).result;
-        const { items, itemSpan, itemStep, blockStart, blockType } = results;
-        if (blockType === BIG_WIG_TYPE_FSTEP) {
-            for (let i = 0; i < items.length; i++) {
-                items[i].start = blockStart + i * itemStep;
-                items[i].end = blockStart + i * itemStep + itemSpan;
-            }
-        }
-        else if (blockType === BIG_WIG_TYPE_VSTEP) {
-            for (let i = 0; i < items.length; i++) {
-                items[i].end = items[i].start + itemSpan;
-            }
+    parseBigWigBlock(buffer, startOffset, request) {
+        const b = buffer.subarray(startOffset);
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        offset += 4;
+        const blockStart = dataView.getInt32(offset, true);
+        offset += 8;
+        const itemStep = dataView.getUint32(offset, true);
+        offset += 4;
+        const itemSpan = dataView.getUint32(offset, true);
+        offset += 4;
+        const blockType = dataView.getUint8(offset);
+        offset += 2;
+        const itemCount = dataView.getUint16(offset, true);
+        offset += 2;
+        const items = new Array(itemCount);
+        switch (blockType) {
+            case 1:
+                for (let i = 0; i < itemCount; i++) {
+                    const start = dataView.getInt32(offset, true);
+                    offset += 4;
+                    const end = dataView.getInt32(offset, true);
+                    offset += 4;
+                    const score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    items[i] = { start, end, score };
+                }
+                break;
+            case 2:
+                for (let i = 0; i < itemCount; i++) {
+                    const start = dataView.getInt32(offset, true);
+                    offset += 4;
+                    const score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    items[i] = { score, start, end: start + itemSpan };
+                }
+                break;
+            case 3:
+                for (let i = 0; i < itemCount; i++) {
+                    const score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    const start = blockStart + i * itemStep;
+                    items[i] = { score, start, end: start + itemSpan };
+                }
+                break;
         }
         return request
-            ? items.filter((f) => BlockView.coordFilter(f, request))
+            ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
             : items;
     }
-    static coordFilter(f, range) {
-        return f.start < range.end && f.end >= range.start;
-    }
     async readFeatures(observer, blocks, opts = {}) {
         try {
             const { blockType, isCompressed } = this;
@@ -279,12 +337,12 @@ export class BlockView {
                 checkAbortSignal(signal);
                 const { length, offset } = blockGroup;
                 const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
-                blockGroup.blocks.forEach((block) => {
+                blockGroup.blocks.forEach(block => {
                     checkAbortSignal(signal);
-                    let blockOffset = block.offset - blockGroup.offset;
+                    let blockOffset = Number(block.offset) - Number(blockGroup.offset);
                     let resultData = data;
                     if (isCompressed) {
-                        resultData = unzip(data.slice(blockOffset));
+                        resultData = unzip(data.subarray(blockOffset));
                         blockOffset = 0;
                     }
                     checkAbortSignal(signal);
@@ -296,9 +354,7 @@ export class BlockView {
                             observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
                             break;
                         case 'bigbed':
-                            observer.next(this.parseBigBedBlock(resultData, blockOffset, 
-                            // eslint-disable-next-line no-bitwise
-                            block.offset * (1 << 8), request));
+                            observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
                             break;
                         default:
                             console.warn(`Don't know what to do with ${blockType}`);

package/esm/blockView.js.map

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

@@ -1,2 +1,2 @@
 /// <reference types="node" />
-export declare function unzip(input: Buffer): Buffer;
+export declare function unzip(input: Buffer): Uint8Array;

package/esm/unzip-pako.js

@@ -1,5 +1,5 @@
-import { inflate } from 'pako';
+import { inflateRaw } from 'pako';
 export function unzip(input) {
-    return Buffer.from(inflate(input));
+    return inflateRaw(input.subarray(2));
 }
 //# sourceMappingURL=unzip-pako.js.map

package/esm/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}

package/esm/util.d.ts

@@ -2,7 +2,17 @@ export declare class AbortError extends Error {
     code: string;
     constructor(message: string);
 }
-export declare function groupBlocks(blocks: any[]): any[];
+export declare function groupBlocks(blocks: {
+    offset: bigint;
+    length: bigint;
+}[]): {
+    blocks: {
+        offset: bigint;
+        length: bigint;
+    }[];
+    length: bigint;
+    offset: bigint;
+}[];
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,

package/esm/util.js

@@ -8,13 +8,18 @@ export class AbortError extends Error {
 // sort blocks by file offset and
 // group blocks that are within 2KB of eachother
 export function groupBlocks(blocks) {
-    blocks.sort((b0, b1) => (b0.offset | 0) - (b1.offset | 0));
+    blocks.sort((b0, b1) => Number(b0.offset) - Number(b1.offset));
     const blockGroups = [];
     let lastBlock;
     let lastBlockEnd;
     for (let i = 0; i < blocks.length; i += 1) {
-        if (lastBlock && blocks[i].offset - lastBlockEnd <= 2000) {
-            lastBlock.length += blocks[i].length - lastBlockEnd + blocks[i].offset;
+        if (lastBlock &&
+            lastBlockEnd &&
+            Number(blocks[i].offset) - lastBlockEnd <= 2000) {
+            lastBlock.length = BigInt(Number(lastBlock.length) +
+                Number(blocks[i].length) -
+                lastBlockEnd +
+                Number(blocks[i].offset));
             lastBlock.blocks.push(blocks[i]);
         }
         else {
@@ -24,7 +29,7 @@ export function groupBlocks(blocks) {
                 offset: blocks[i].offset,
             }));
         }
-        lastBlockEnd = lastBlock.offset + lastBlock.length;
+        lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
     }
     return blockGroups;
 }

package/esm/util.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "1.0.35",
+  "version": "2.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -41,21 +41,19 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/binary-parser": "^1.4.0",
     "abortable-promise-cache": "^1.4.1",
-    "buffer-crc32": "^0.2.13",
-    "es6-promisify": "^6.0.1",
+    "binary-parser": "^2.1.0",
     "generic-filehandle": "^2.0.0",
-    "pako": "^1.0.0",
+    "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
     "rxjs": "^6.5.2"
   },
   "devDependencies": {
     "@gmod/bed": "^2.0.0",
-    "@types/jest": "^27.0.3",
+    "@types/jest": "^28.1.4",
     "@types/long": "^4.0.0",
-    "@types/node": "^12.0.2",
-    "@types/pako": "^1.0.3",
+    "@types/node": "^18.0.0",
+    "@types/pako": "^2.0.0",
     "@typescript-eslint/eslint-plugin": "^5.10.0",
     "@typescript-eslint/parser": "^5.10.0",
     "cross-fetch": "^3.0.2",
@@ -63,11 +61,12 @@
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^27.4.3",
+    "jest": "^28.1.2",
+    "jest-environment-jsdom": "^28.1.2",
     "prettier": "^2.5.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.11",
-    "ts-jest": "^27.0.7",
+    "ts-jest": "^28.0.5",
     "typescript": "^4.5.2"
   },
   "publishConfig": {