@gmod/bbi 4.0.6 → 5.0.1

package/esm/bigbed.js

@@ -1,9 +1,9 @@
 import { Buffer } from 'buffer';
-import { Parser } from 'binary-parser';
 import { Observable, merge, firstValueFrom } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
+// locals
 import { BBI } from './bbi';
 export function filterUndef(ts) {
     return ts.filter((t) => !!t);
@@ -28,43 +28,50 @@ export class BigBed extends BBI {
     }
     /*
      * parse the bigbed extraIndex fields
-     * @param abortSignal to abort operation
-     * @return a Promise for an array of Index data structure since there can be multiple extraIndexes in a bigbed, see bedToBigBed documentation
+     *
+     *
+     * @return a Promise for an array of Index data structure since there can be
+     * multiple extraIndexes in a bigbed, see bedToBigBed documentation
      */
     async _readIndices(opts) {
         const { extHeaderOffset, isBigEndian } = await this.getHeader(opts);
         const { buffer: data } = await this.bbi.read(Buffer.alloc(64), 0, 64, Number(extHeaderOffset));
-        const le = isBigEndian ? 'big' : 'little';
-        const ret = new Parser()
-            .endianess(le)
-            .uint16('size')
-            .uint16('count')
-            .uint64('offset')
-            .parse(data);
-        const { count, offset } = ret;
+        const le = !isBigEndian;
+        const b = data;
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        // const _size = dataView.getUint16(offset, le)
+        offset += 2;
+        const count = dataView.getUint16(offset, le);
+        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 } = await this.bbi.read(Buffer.alloc(len), 0, len, Number(offset));
-        const extParser = new Parser()
-            .endianess(le)
-            .int16('type')
-            .int16('fieldcount')
-            .uint64('offset')
-            .skip(4)
-            .int16('field');
+        const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, Number(dataOffset));
         const indices = [];
         for (let i = 0; i < count; i += 1) {
-            indices.push(extParser.parse(buffer.subarray(i * blocklen)));
+            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;
     }
     /*
-     * perform a search in the bigbed extraIndex to find which blocks in the bigbed data to look for the
-     * actual feature data
+     * 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
@@ -77,52 +84,48 @@ export class BigBed extends BBI {
             return [];
         }
         const locs = indices.map(async (index) => {
-            const { offset, field } = index;
-            const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, Number(offset), opts);
-            const le = isBigEndian ? 'big' : 'little';
-            const p = new Parser()
-                .endianess(le)
-                .int32('magic')
-                .int32('blockSize')
-                .int32('keySize')
-                .int32('valSize')
-                .uint64('itemCount');
-            const { blockSize, keySize, valSize } = p.parse(data);
-            // console.log({blockSize,keySize,valSize})
-            const bpt = new Parser()
-                .endianess(le)
-                .int8('nodeType')
-                .skip(1)
-                .int16('cnt')
-                .choice({
-                tag: 'nodeType',
-                choices: {
-                    0: new Parser().array('leafkeys', {
-                        length: 'cnt',
-                        type: new Parser()
-                            .endianess(le)
-                            .string('key', { length: keySize, stripNull: true })
-                            .uint64('offset'),
-                    }),
-                    1: new Parser().array('keys', {
-                        length: 'cnt',
-                        type: new Parser()
-                            .endianess(le)
-                            .string('key', { length: keySize, stripNull: true })
-                            .uint64('offset')
-                            .uint32('length')
-                            .uint32('reserved'),
-                    }),
-                },
-            });
+            const { offset: offset2, field } = index;
+            const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, offset2, opts);
+            const le = !isBigEndian;
+            const b = data;
+            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 = async (nodeOffset) => {
                 const val = Number(nodeOffset);
                 const len = 4 + blockSize * (keySize + valSize);
                 const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, val, opts);
-                const node = bpt.parse(buffer);
-                if (node.leafkeys) {
-                    let lastOffset;
-                    for (const { key, offset } of node.leafkeys) {
+                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);
                         }
@@ -130,15 +133,31 @@ export class BigBed extends BBI {
                     }
                     return bptReadNode(lastOffset);
                 }
-                for (const n of node.keys) {
-                    if (n.key === name) {
-                        return { ...n, field };
+                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 });
+                    }
+                    for (const n of keys) {
+                        if (n.key === name) {
+                            return { ...n, field };
+                        }
                     }
+                    return undefined;
                 }
-                return undefined;
             };
             const rootNodeOffset = 32;
-            return bptReadNode(Number(offset) + rootNodeOffset);
+            return bptReadNode(offset2 + rootNodeOffset);
         });
         return filterUndef(await Promise.all(locs));
     }

package/esm/bigbed.js.map

@@ -1 +1 @@
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package/esm/bigint-polyfill/polyfill.js

@@ -1,4 +1,4 @@
-import { getBigInt64, getBigUint64, setBigInt64, setBigUint64 } from './pure';
+import { getBigInt64, getBigUint64 } from './pure';
 if (!('getBigInt64' in DataView)) {
     DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
         return getBigInt64(this, byteOffset, littleEndian);
@@ -9,14 +9,4 @@ if (!('getBigUint64' in DataView)) {
         return getBigUint64(this, byteOffset, littleEndian);
     };
 }
-if (!('setBigInt64' in DataView)) {
-    DataView.prototype.setBigInt64 = function (byteOffset, value, littleEndian) {
-        setBigInt64(this, byteOffset, value, littleEndian);
-    };
-}
-if (!('setBigUint64' in DataView)) {
-    DataView.prototype.setBigUint64 = function (byteOffset, value, littleEndian) {
-        setBigUint64(this, byteOffset, value, littleEndian);
-    };
-}
 //# sourceMappingURL=polyfill.js.map

package/esm/bigint-polyfill/polyfill.js.map

@@ -1 +1 @@
-{"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAE7E,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACxE,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACzE,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}
+{"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAElD,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}

package/esm/bigint-polyfill/pure.d.ts

@@ -1,4 +1,2 @@
 export declare function getBigInt64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
 export declare function getBigUint64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
-export declare function setBigInt64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;
-export declare function setBigUint64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;

package/esm/bigint-polyfill/pure.js

@@ -19,28 +19,4 @@ export function getBigUint64(dataView, byteOffset, littleEndian) {
     return ((BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
         BigInt(a * littleEndianMask + b * bigEndianMask));
 }
-export function setBigInt64(dataView, byteOffset, value, littleEndian) {
-    const hi = Number(value >> BigInt32);
-    const lo = Number(value & BigInt(0xffffffff));
-    if (littleEndian) {
-        dataView.setInt32(byteOffset + 4, hi, littleEndian);
-        dataView.setUint32(byteOffset, lo, littleEndian);
-    }
-    else {
-        dataView.setInt32(byteOffset, hi, littleEndian);
-        dataView.setUint32(byteOffset + 4, lo, littleEndian);
-    }
-}
-export function setBigUint64(dataView, byteOffset, value, littleEndian) {
-    const hi = Number(value >> BigInt32);
-    const lo = Number(value & BigInt(0xffffffff));
-    if (littleEndian) {
-        dataView.setUint32(byteOffset + 4, hi, littleEndian);
-        dataView.setUint32(byteOffset, lo, littleEndian);
-    }
-    else {
-        dataView.setUint32(byteOffset, hi, littleEndian);
-        dataView.setUint32(byteOffset + 4, lo, littleEndian);
-    }
-}
 //# sourceMappingURL=pure.js.map

package/esm/bigint-polyfill/pure.js.map

@@ -1 +1 @@
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+{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;AAE3B,MAAM,UAAU,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,OAAO,CACL,CAAC,MAAM,CACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,aAAa;QACzD,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,gBAAgB,CACrE;QACC,QAAQ,CAAC;QACX,MAAM,CACJ,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,gBAAgB;YAC7D,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,aAAa,CACnE,CACF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,CAAA;IAE1D,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,4EAA4E;IAC5E,gDAAgD;IAChD,kCAAkC;IAClC,OAAO,CACL,CAAC,MAAM,CAAC,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,gBAAgB,CAAC,IAAI,QAAQ,CAAC;QAC9D,MAAM,CAAC,CAAC,GAAG,gBAAgB,GAAG,CAAC,GAAG,aAAa,CAAC,CACjD,CAAA;AACH,CAAC"}

package/esm/bigwig.js

@@ -10,18 +10,13 @@ export class BigWig extends BBI {
      * or scale used to infer the zoomLevel to use
      */
     async getView(scale, opts) {
-        const { zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize } = await this.getHeader(opts);
+        const { zoomLevels, refsByName, isBigEndian, uncompressBufSize } = await this.getHeader(opts);
         const basesPerPx = 1 / scale;
-        let maxLevel = zoomLevels.length;
-        if (!fileSize) {
-            // if we don't know the file size, we can't fetch the highest zoom level :-(
-            maxLevel -= 1;
-        }
+        const maxLevel = zoomLevels.length - 1;
         for (let i = maxLevel; i >= 0; i -= 1) {
             const zh = zoomLevels[i];
             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                const indexOffset = Number(zh.indexOffset);
-                return new BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
+                return new BlockView(this.bbi, refsByName, zh.indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
             }
         }
         return this.getUnzoomedView(opts);

package/esm/bigwig.js.map

@@ -1 +1 @@
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+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAC9D,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,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/esm/block-view.d.ts

@@ -13,8 +13,8 @@ interface Options {
 /**
  * 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 declare class BlockView {
@@ -26,16 +26,14 @@ export declare class BlockView {
     private blockType;
     private cirTreePromise?;
     private featureCache;
-    private leafParser;
-    private bigBedParser;
     constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;
     private parseBigWigBlock;
     readFeatures(observer: Observer<Feature[]>, blocks: {
-        offset: bigint;
-        length: bigint;
+        offset: number;
+        length: number;
     }[], opts?: Options): Promise<void>;
 }
 export {};