@gmod/bbi 4.0.6 → 5.0.0

package/esm/block-view.js

@@ -1,115 +1,18 @@
 import { Buffer } from 'buffer';
-import { Parser } from 'binary-parser';
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 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()
-        .endianess(le)
-        .uint32('chromId')
-        .uint32('start')
-        .uint32('end')
-        .uint32('validCnt')
-        .floatle('minScore')
-        .floatle('maxScore')
-        .floatle('sumData')
-        .floatle('sumSqData')
-        .saveOffset('offset');
-    const leafParser = new Parser()
-        .endianess(le)
-        .uint8('isLeaf')
-        .skip(1)
-        .uint16('cnt')
-        .choice({
-        tag: 'isLeaf',
-        choices: {
-            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')
-                    .saveOffset('offset'),
-            }),
-            0: new Parser().array('recurOffsets', {
-                length: 'cnt',
-                type: new Parser()
-                    .endianess(le)
-                    .uint32('startChrom')
-                    .uint32('startBase')
-                    .uint32('endChrom')
-                    .uint32('endBase')
-                    .uint64('blockOffset')
-                    .saveOffset('offset'),
-            }),
-        },
-    });
-    const bigBedParser = new Parser()
-        .endianess(le)
-        .uint32('chromId')
-        .int32('start')
-        .int32('end')
-        .string('rest', {
-        zeroTerminated: true,
-    })
-        .saveOffset('offset');
-    const bigWigParser = new Parser()
-        .endianess(le)
-        .skip(4)
-        .int32('blockStart')
-        .skip(4)
-        .uint32('itemStep')
-        .uint32('itemSpan')
-        .uint8('blockType')
-        .skip(1)
-        .uint16('itemCount')
-        .choice({
-        tag: 'blockType',
-        choices: {
-            [BIG_WIG_TYPE_FSTEP]: new Parser().array('items', {
-                length: 'itemCount',
-                type: new Parser().floatle('score'),
-            }),
-            [BIG_WIG_TYPE_VSTEP]: new Parser().array('items', {
-                length: 'itemCount',
-                type: new Parser().endianess(le).int32('start').floatle('score'),
-            }),
-            [BIG_WIG_TYPE_GRAPH]: new Parser().array('items', {
-                length: 'itemCount',
-                type: new Parser()
-                    .endianess(le)
-                    .int32('start')
-                    .int32('end')
-                    .floatle('score'),
-            }),
-        },
-    });
-    return {
-        bigWigParser,
-        bigBedParser,
-        summaryParser,
-        leafParser,
-    };
-}
 /**
  * View into a subset of the data in a BigWig file.
  *
- * Adapted by Robert Buels and Colin Diesh from bigwig.js in the Dalliance Genome
- * Explorer by Thomas Down.
+ * Adapted by Robert Buels and Colin Diesh from bigwig.js in the Dalliance
+ * Genome Explorer by Thomas Down.
  * @constructs
  */
 export class BlockView {
@@ -123,8 +26,8 @@ export class BlockView {
         this.featureCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1000 }),
             fill: async (requestData, signal) => {
-                const len = Number(requestData.length);
-                const off = Number(requestData.offset);
+                const len = requestData.length;
+                const off = requestData.offset;
                 const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, off, {
                     signal,
                 });
@@ -134,9 +37,6 @@ export class BlockView {
         if (!(cirTreeOffset >= 0)) {
             throw new Error('invalid cirTreeOffset!');
         }
-        const parsers = getParsers(isBigEndian);
-        this.leafParser = parsers.leafParser;
-        this.bigBedParser = parsers.bigBedParser;
     }
     async readWigData(chrName, start, end, observer, opts) {
         try {
@@ -147,7 +47,7 @@ export class BlockView {
             }
             const request = { chrId, start, end };
             if (!this.cirTreePromise) {
-                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
+                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, cirTreeOffset, opts);
             }
             const { buffer } = await this.cirTreePromise;
             const cirBlockSize = isBigEndian
@@ -155,24 +55,76 @@ export class BlockView {
                 : buffer.readUInt32LE(4);
             let blocksToFetch = [];
             let outstanding = 0;
-            const cirFobRecur2 = (cirBlockData, offset, level) => {
+            const le = true;
+            const cirFobRecur2 = (cirBlockData, offset2, level) => {
                 try {
-                    const data = cirBlockData.subarray(offset);
-                    const p = this.leafParser.parse(data);
-                    if (p.blocksToFetch) {
-                        blocksToFetch = blocksToFetch.concat(p.blocksToFetch
+                    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,
                         })));
                     }
-                    if (p.recurOffsets) {
-                        const recurOffsets = p.recurOffsets
+                    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 => Number(l.blockOffset));
-                        if (recurOffsets.length > 0) {
-                            cirFobRecur(recurOffsets, level + 1);
+                            .map(l => l.blockOffset);
+                        if (recurOffsets2.length > 0) {
+                            cirFobRecur(recurOffsets2, level + 1);
                         }
                     }
                 }
@@ -211,13 +163,19 @@ export class BlockView {
                 try {
                     outstanding += offset.length;
                     // Upper bound on size, based on a completely full leaf node.
-                    const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32;
+                    const maxCirBlockSpan = 4 + cirBlockSize * 32;
                     let spans = new Range([
-                        { min: offset[0], max: offset[0] + maxCirBlockSpan },
+                        {
+                            min: offset[0],
+                            max: offset[0] + maxCirBlockSpan,
+                        },
                     ]);
                     for (let i = 1; i < offset.length; i += 1) {
                         const blockSpan = new Range([
-                            { min: offset[i], max: offset[i] + maxCirBlockSpan },
+                            {
+                                min: offset[i],
+                                max: offset[i] + maxCirBlockSpan,
+                            },
                         ]);
                         spans = spans.union(blockSpan);
                     }
@@ -234,11 +192,11 @@ export class BlockView {
             observer.error(e);
         }
     }
-    parseSummaryBlock(buffer, startOffset, request) {
+    parseSummaryBlock(b, startOffset, request) {
         const features = [];
         let offset = startOffset;
-        const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
-        while (offset < buffer.byteLength) {
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        while (offset < b.byteLength) {
             // this was extracted from looking at the runtime code generated by
             // binary-parser
             const chromId = dataView.getUint32(offset, true);
@@ -277,17 +235,38 @@ export 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 res = this.bigBedParser.parse(data.subarray(currOffset));
-            res.uniqueId = `bb-${offset + currOffset}`;
-            items.push(res);
-            currOffset += res.offset;
+            const c2 = currOffset;
+            const chromId = dataView.getUint32(currOffset, le);
+            currOffset += 4;
+            const start = dataView.getInt32(currOffset, le);
+            currOffset += 4;
+            const end = dataView.getInt32(currOffset, le);
+            currOffset += 4;
+            let i = currOffset;
+            for (; i < data.length; i++) {
+                if (data[i] === 0) {
+                    break;
+                }
+            }
+            const rest = data.subarray(currOffset, i).toString();
+            currOffset = i + 1;
+            items.push({
+                chromId,
+                start,
+                end,
+                rest,
+                uniqueId: `bb-${offset + c2}`,
+            });
         }
         return request
             ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
             : items;
     }
-    parseBigWigBlock(buffer, startOffset, request) {
+    parseBigWigBlock(buffer, startOffset, req) {
         const b = buffer.subarray(startOffset);
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         let offset = 0;
@@ -312,7 +291,11 @@ export class BlockView {
                     offset += 4;
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
-                    items[i] = { start, end, score };
+                    items[i] = {
+                        start,
+                        end,
+                        score,
+                    };
                 }
                 break;
             }
@@ -322,7 +305,11 @@ export class BlockView {
                     offset += 4;
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
-                    items[i] = { score, start, end: start + itemSpan };
+                    items[i] = {
+                        score,
+                        start,
+                        end: start + itemSpan,
+                    };
                 }
                 break;
             }
@@ -331,13 +318,17 @@ export class BlockView {
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
                     const start = blockStart + i * itemStep;
-                    items[i] = { score, start, end: start + itemSpan };
+                    items[i] = {
+                        score,
+                        start,
+                        end: start + itemSpan,
+                    };
                 }
                 break;
             }
         }
-        return request
-            ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
+        return req
+            ? items.filter(f => coordFilter(f.start, f.end, req.start, req.end))
             : items;
     }
     async readFeatures(observer, blocks, opts = {}) {

package/esm/block-view.js.map

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package/esm/range.js

@@ -10,7 +10,7 @@ export default class Range {
         return this.ranges[0].min;
     }
     get max() {
-        return this.ranges[this.ranges.length - 1].max;
+        return this.ranges.at(-1).max;
     }
     contains(pos) {
         for (const r of this.ranges) {

package/esm/range.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -2,22 +2,19 @@ export declare class AbortError extends Error {
     code: string;
     constructor(message: string);
 }
-export declare function groupBlocks(blocks: {
-    offset: bigint;
-    length: bigint;
-}[]): {
-    blocks: {
-        offset: bigint;
-        length: bigint;
-    }[];
-    length: bigint;
-    offset: bigint;
+interface Block {
+    offset: number;
+    length: number;
+}
+export declare function groupBlocks(blocks: Block[]): {
+    blocks: Block[];
+    length: number;
+    offset: number;
 }[];
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -32,3 +29,4 @@ export declare function checkAbortSignal(signal?: AbortSignal): void;
  * @param {AbortSignal} signal
  */
 export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
+export {};

package/esm/util.js

@@ -7,18 +7,14 @@ 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) => Number(b0.offset) - Number(b1.offset));
+    blocks.sort((b0, b1) => b0.offset - b1.offset);
     const blockGroups = [];
     let lastBlock;
     let lastBlockEnd;
     for (const block of blocks) {
-        if (lastBlock &&
-            lastBlockEnd &&
-            Number(block.offset) - lastBlockEnd <= 2000) {
-            lastBlock.length = BigInt(Number(lastBlock.length) +
-                Number(block.length) -
-                lastBlockEnd +
-                Number(block.offset));
+        if (lastBlock && lastBlockEnd && block.offset - lastBlockEnd <= 2000) {
+            lastBlock.length =
+                lastBlock.length + block.length - lastBlockEnd + block.offset;
             lastBlock.blocks.push(block);
         }
         else {
@@ -28,15 +24,14 @@ export function groupBlocks(blocks) {
                 offset: block.offset,
             }));
         }
-        lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
+        lastBlockEnd = lastBlock.offset + lastBlock.length;
     }
     return blockGroups;
 }
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -48,7 +43,6 @@ export function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        // console.log('bam aborted!')
         if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';

package/esm/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,UAAW,SAAQ,KAAK;IAGnC,YAAmB,OAAe;QAChC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,aAAa,CAAA;IAC3B,CAAC;CACF;AAMD,iCAAiC;AACjC,gDAAgD;AAChD,MAAM,UAAU,WAAW,CAAC,MAAe;IACzC,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,CAAA;IAE9C,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAoD,CAAA;IACxD,IAAI,YAAgC,CAAA;IACpC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,SAAS,IAAI,YAAY,IAAI,KAAK,CAAC,MAAM,GAAG,YAAY,IAAI,IAAI,EAAE,CAAC;YACrE,SAAS,CAAC,MAAM;gBACd,SAAS,CAAC,MAAM,GAAG,KAAK,CAAC,MAAM,GAAG,YAAY,GAAG,KAAK,CAAC,MAAM,CAAA;YAC/D,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC9B,CAAC;aAAM,CAAC;YACN,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,KAAK,CAAC;gBACf,MAAM,EAAE,KAAK,CAAC,MAAM;gBACpB,MAAM,EAAE,KAAK,CAAC,MAAM;aACrB,CAAC,CACH,CAAA;QACH,CAAC;QACD,YAAY,GAAG,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACpD,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "4.0.6",
+  "version": "5.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -43,7 +43,6 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "binary-parser": "^2.1.0",
     "generic-filehandle": "^3.0.0",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
@@ -54,12 +53,12 @@
     "@types/jest": "^29.5.12",
     "@types/node": "^20.11.16",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^7.3.1",
-    "@typescript-eslint/parser": "^7.3.1",
+    "@typescript-eslint/eslint-plugin": "^8.0.1",
+    "@typescript-eslint/parser": "^8.0.1",
     "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^54.0.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.6.2",
     "jest-environment-jsdom": "^29.6.2",
     "prettier": "^3.2.5",