@gmod/bbi 9.0.9 → 9.0.12

package/README.md

@@ -75,7 +75,7 @@ See the [example](./example/) folder for a complete working demo.
 Accepts an object containing either
 
 - path - path to a local file
-- url - path to a url
+- url - URL of a remote file
 - filehandle - a filehandle instance that you can implement as a custom class
   yourself. path and url are based on
   https://www.npmjs.com/package/generic-filehandle2 but by implementing a class
@@ -94,7 +94,7 @@ Accepts an object containing either
   zoom level that is returned is the one which has reductionLevel<=2/opts.scale
   (reductionLevel is a property of the zoom level structure in the bigwig file
   data)
-- opts.basesPerScale - optional, inverse of opts.scale e.g. bpPerPx
+- opts.basesPerSpan - optional, inverse of opts.scale (bp per pixel)
 - opts.signal - optional, an AbortSignal to halt processing
 
 Returns a promise to an array of features. If an incorrect refName or no
@@ -105,8 +105,8 @@ Example:
 ```typescript
 const feats = await bigwig.getFeatures('chr1', 0, 100)
 // returns array of features with start, end, score
-// coordinates on returned data are are 0-based half open
-// no conversion to 1-based as in wig is done)
+// coordinates on returned data are 0-based half open
+// no conversion to 1-based as in wig is done
 // note refseq is not returned on the object, it is clearly chr1 from the query though
 ```
 
@@ -116,13 +116,17 @@ Here is what the reductionLevel structure looks like in a file. The zoomLevel
 that is chosen is the first reductionLevel<2\*opts.basesPerScale (or
 reductionLevel<2/opts.scale) when scanning backwards through this list
 
-      [ { reductionLevel: 40, ... },
-        { reductionLevel: 160, ... },
-        { reductionLevel: 640, ... },
-        { reductionLevel: 2560, ... },
-        { reductionLevel: 10240, ... },
-        { reductionLevel: 40960, ... },
-        { reductionLevel: 163840, ... } ]
+```json
+[
+  { "reductionLevel": 40 },
+  { "reductionLevel": 160 },
+  { "reductionLevel": 640 },
+  { "reductionLevel": 2560 },
+  { "reductionLevel": 10240 },
+  { "reductionLevel": 40960 },
+  { "reductionLevel": 163840 }
+]
+```
 
 #### getFeaturesAsArrays(refName, start, end, opts)
 
@@ -199,7 +203,7 @@ they exist.
 - opts.signal - optional, an AbortSignal to halt processing
 
 returns a promise to an array of features. no concept of zoom levels is used
-with bigwig data
+with bigbed data
 
 #### searchExtraIndex(name, opts)
 
@@ -273,6 +277,60 @@ Features after parsing with @gmod/bed:
 }
 ```
 
+### parseBigWig(bigwig, opts)
+
+A convenience function that reads all features from every chromosome in a BigWig
+file, returning non-empty base-resolution results only (no zoom levels).
+
+- bigwig - a `BigWig` instance
+- opts - optional `RequestOptions` (e.g. `opts.signal` for abort)
+
+Returns a `Promise<BigWigFeatureArrays[]>`, one entry per chromosome that has
+data.
+
+```typescript
+import { BigWig, parseBigWig } from '@gmod/bbi'
+
+const file = new BigWig({ path: 'volvox.bw' })
+const results = await parseBigWig(file)
+for (const { starts, ends, scores } of results) {
+  for (let i = 0; i < starts.length; i++) {
+    console.log(starts[i], ends[i], scores[i])
+  }
+}
+```
+
+### ArrayFeatureView / BigWigFeature
+
+`ArrayFeatureView` wraps a `BigWigFeatureArrays` or `SummaryFeatureArrays`
+result and exposes a JBrowse-compatible `Feature`-style interface.
+`BigWigFeature` is a single-feature view into an `ArrayFeatureView`.
+
+```typescript
+import { BigWig, ArrayFeatureView } from '@gmod/bbi'
+
+const file = new BigWig({ path: 'volvox.bw' })
+const arrays = await file.getFeaturesAsArrays('chr1', 0, 100000)
+const view = new ArrayFeatureView(arrays, 'mySource', 'chr1')
+
+for (let i = 0; i < view.length; i++) {
+  console.log(view.start(i), view.end(i), view.score(i))
+}
+```
+
+`BigWigFeature` instances are also iterable via `view.get(i, key)` and expose a
+`toJSON()` method. Keys: `start`, `end`, `score`, `refName`, `source`,
+`summary`, `minScore`, `maxScore`.
+
+## Publishing
+
+[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
+Actions.
+
+```bash
+pnpm version patch  # or minor/major
+```
+
 ## Academic Use
 
 This package was written with funding from the [NHGRI](http://genome.gov) as

package/dist/array-feature-view.d.ts

@@ -7,7 +7,7 @@ export declare class BigWigFeature {
     get(key: 'start' | 'end' | 'score'): number;
     get(key: 'minScore' | 'maxScore'): number | undefined;
     get(key: 'summary'): boolean;
-    get(key: string): any;
+    get(key: string): string | number | boolean | undefined;
     id(): string;
     toJSON(): {
         start: number;
@@ -28,12 +28,10 @@ export declare class ArrayFeatureView {
     readonly minScores: Float32Array | undefined;
     readonly maxScores: Float32Array | undefined;
     readonly isSummary: boolean;
-    private _source;
-    private _refName;
+    readonly source: string;
+    readonly refName: string;
     constructor(arrays: BigWigFeatureArrays | SummaryFeatureArrays, source: string, refName: string);
     get length(): number;
-    get source(): string;
-    get refName(): string;
     start(i: number): number;
     end(i: number): number;
     score(i: number): number;
@@ -41,7 +39,8 @@ export declare class ArrayFeatureView {
     maxScore(i: number): number | undefined;
     id(i: number): string;
     get(i: number, key: 'refName' | 'source'): string;
-    get(i: number, key: 'start' | 'end' | 'score' | 'minScore' | 'maxScore'): number | undefined;
+    get(i: number, key: 'start' | 'end' | 'score'): number;
+    get(i: number, key: 'minScore' | 'maxScore'): number | undefined;
     get(i: number, key: 'summary'): boolean;
     get(i: number, key: string): string | number | boolean | undefined;
 }

package/dist/array-feature-view.js

@@ -37,8 +37,8 @@ class ArrayFeatureView {
     minScores;
     maxScores;
     isSummary;
-    _source;
-    _refName;
+    source;
+    refName;
     constructor(arrays, source, refName) {
         this.starts = arrays.starts;
         this.ends = arrays.ends;
@@ -46,18 +46,12 @@ class ArrayFeatureView {
         this.isSummary = arrays.isSummary;
         this.minScores = arrays.isSummary ? arrays.minScores : undefined;
         this.maxScores = arrays.isSummary ? arrays.maxScores : undefined;
-        this._source = source;
-        this._refName = refName;
+        this.source = source;
+        this.refName = refName;
     }
     get length() {
         return this.starts.length;
     }
-    get source() {
-        return this._source;
-    }
-    get refName() {
-        return this._refName;
-    }
     start(i) {
         return this.starts[i];
     }
@@ -74,7 +68,7 @@ class ArrayFeatureView {
         return this.maxScores?.[i];
     }
     id(i) {
-        return `${this._source}:${this._refName}:${this.starts[i]}-${this.ends[i]}`;
+        return `${this.source}:${this.refName}:${this.starts[i]}-${this.ends[i]}`;
     }
     get(i, key) {
         switch (key) {
@@ -85,9 +79,9 @@ class ArrayFeatureView {
             case 'score':
                 return this.scores[i];
             case 'refName':
-                return this._refName;
+                return this.refName;
             case 'source':
-                return this._source;
+                return this.source;
             case 'minScore':
                 return this.minScores?.[i];
             case 'maxScore':

package/dist/array-feature-view.js.map

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package/dist/bbi.js

@@ -3,12 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
 const generic_filehandle2_1 = require("generic-filehandle2");
 const block_view_ts_1 = require("./block-view.js");
+const util_ts_1 = require("./util.js");
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
 const decoder = new TextDecoder('utf8');
-function getDataView(buffer) {
-    return new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
-}
 class BBI {
     bbi;
     headerP;
@@ -58,7 +56,7 @@ class BBI {
     }
     async _getMainHeader(opts, requestSize = 2000) {
         const b = await this.bbi.read(requestSize, 0, opts);
-        const dataView = getDataView(b);
+        const dataView = (0, util_ts_1.getDataView)(b);
         let offset = 0;
         const magic = dataView.getInt32(offset, true);
         offset += 4;
@@ -92,15 +90,13 @@ class BBI {
         for (let i = 0; i < numZoomLevels; i++) {
             const reductionLevel = dataView.getUint32(offset, true);
             offset += 4;
-            const reserved = dataView.getUint32(offset, true);
-            offset += 4;
+            offset += 4; // reserved
             const dataOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
             const indexOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
             zoomLevels.push({
                 reductionLevel,
-                reserved,
                 dataOffset,
                 indexOffset,
             });
@@ -113,29 +109,24 @@ class BBI {
         }
         let totalSummary;
         if (totalSummaryOffset) {
-            const b2 = b.subarray(totalSummaryOffset);
-            let offset = 0;
-            const dataView = getDataView(b2);
-            const basesCovered = Number(dataView.getBigUint64(offset, true));
-            offset += 8;
-            const scoreMin = dataView.getFloat64(offset, true);
-            offset += 8;
-            const scoreMax = dataView.getFloat64(offset, true);
-            offset += 8;
-            const scoreSum = dataView.getFloat64(offset, true);
-            offset += 8;
-            const scoreSumSquares = dataView.getFloat64(offset, true);
+            const summaryView = (0, util_ts_1.getDataView)(b, totalSummaryOffset);
             totalSummary = {
-                scoreMin,
-                scoreMax,
-                scoreSum,
-                scoreSumSquares,
-                basesCovered,
+                basesCovered: Number(summaryView.getBigUint64(0, true)),
+                scoreMin: summaryView.getFloat64(8, true),
+                scoreMax: summaryView.getFloat64(16, true),
+                scoreSum: summaryView.getFloat64(24, true),
+                scoreSumSquares: summaryView.getFloat64(32, true),
             };
         }
         else {
             throw new Error('no stats');
         }
+        let autoSql = '';
+        if (asOffset) {
+            const nullPos = b.indexOf(0, asOffset);
+            const end = nullPos === -1 ? b.length : nullPos;
+            autoSql = decoder.decode(b.subarray(asOffset, end));
+        }
         return {
             zoomLevels,
             magic,
@@ -152,9 +143,7 @@ class BBI {
             unzoomedIndexOffset,
             fileType,
             version,
-            autoSql: asOffset
-                ? decoder.decode(b.subarray(asOffset, b.indexOf(0, asOffset)))
-                : '',
+            autoSql,
         };
     }
     // Reads the B+ tree that maps chromosome names to integer IDs
@@ -164,25 +153,21 @@ class BBI {
         const refsByNumber = [];
         const refsByName = {};
         const chromosomeTreeOffset = header.chromosomeTreeOffset;
-        const dataView = getDataView(await this.bbi.read(32, chromosomeTreeOffset, opts));
+        const dataView = (0, util_ts_1.getDataView)(await this.bbi.read(32, chromosomeTreeOffset, opts));
         const keySize = dataView.getUint32(8, true);
         const valSize = dataView.getUint32(12, true);
         // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
         const readBPlusTreeNode = async (currentOffset) => {
-            const header = getDataView(await this.bbi.read(4, currentOffset));
+            const header = (0, util_ts_1.getDataView)(await this.bbi.read(4, currentOffset, opts));
             const isLeafNode = header.getUint8(0);
             const count = header.getUint16(2, true);
             // Leaf nodes contain the actual chromosome name-to-ID mappings
             if (isLeafNode) {
-                const b = await this.bbi.read(count * (keySize + valSize), currentOffset + 4);
-                const dataView = getDataView(b);
+                const b = await this.bbi.read(count * (keySize + valSize), currentOffset + 4, opts);
+                const dataView = (0, util_ts_1.getDataView)(b);
                 let offset = 0;
                 for (let n = 0; n < count; n++) {
-                    const keyEnd = b.indexOf(0, offset);
-                    const effectiveKeyEnd = keyEnd !== -1 && keyEnd < offset + keySize
-                        ? keyEnd
-                        : offset + keySize;
-                    const key = decoder.decode(b.subarray(offset, effectiveKeyEnd));
+                    const key = (0, util_ts_1.parseKey)(b, offset, keySize);
                     offset += keySize;
                     const refId = dataView.getUint32(offset, true);
                     offset += 4;
@@ -194,7 +179,7 @@ class BBI {
             }
             else {
                 // Non-leaf nodes contain pointers to child nodes
-                const dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + 4));
+                const dataView = (0, util_ts_1.getDataView)(await this.bbi.read(count * (keySize + 8), currentOffset + 4, opts));
                 const nextNodes = [];
                 let offset = 0;
                 for (let n = 0; n < count; n++) {

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigbed.d.ts

@@ -1,4 +1,3 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { BBI } from './bbi.ts';
 import type { RequestOptions } from './types.ts';
 interface Index {
@@ -8,7 +7,7 @@ interface Index {
     field: number;
 }
 export declare class BigBed extends BBI {
-    readIndicesCache: AbortablePromiseCache<RequestOptions, Index[], string>;
+    private indicesP?;
     readIndices(opts?: RequestOptions): Promise<Index[]>;
     protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view.ts").BlockView>;
     private _readIndices;

package/dist/bigbed.js

@@ -1,13 +1,8 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = void 0;
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
-const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
 const bbi_ts_1 = require("./bbi.js");
-const decoder = new TextDecoder('utf8');
+const util_ts_1 = require("./util.js");
 function getTabField(str, fieldIndex) {
     if (fieldIndex < 0) {
         return undefined;
@@ -23,18 +18,12 @@ function getTabField(str, fieldIndex) {
     const end = str.indexOf('\t', start);
     return end === -1 ? str.slice(start) : str.slice(start, end);
 }
-// Parses a null-terminated string key from a B+ tree node
-function parseKey(buffer, offset, keySize) {
-    const keyEnd = buffer.indexOf(0, offset);
-    const effectiveKeyEnd = keyEnd !== -1 && keyEnd < offset + keySize ? keyEnd : offset + keySize;
-    return decoder.decode(buffer.subarray(offset, effectiveKeyEnd));
-}
 // Recursively traverses a B+ tree to search for a specific name in the BigBed extraIndex
 // B+ trees are balanced tree structures optimized for disk-based searches
 async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, name, field, opts) {
     const len = 4 + blockSize * (keySize + valSize);
     const buffer = await bbi.read(len, nodeOffset, opts);
-    const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+    const dataView = (0, util_ts_1.getDataView)(buffer);
     const nodeType = dataView.getInt8(0);
     const cnt = dataView.getInt16(2, true);
     let offset = 4;
@@ -42,7 +31,7 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
     if (nodeType === 0) {
         const leafkeys = [];
         for (let i = 0; i < cnt; i++) {
-            const key = parseKey(buffer, offset, keySize);
+            const key = (0, util_ts_1.parseKey)(buffer, offset, keySize);
             offset += keySize;
             const dataOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
@@ -51,29 +40,27 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
                 offset: dataOffset,
             });
         }
-        // Binary search to find the appropriate child node
         let left = 0;
         let right = leafkeys.length - 1;
-        let targetIndex = leafkeys.length - 1;
+        let targetIndex = -1;
         while (left <= right) {
             const mid = Math.floor((left + right) / 2);
-            const cmp = name.localeCompare(leafkeys[mid].key);
-            if (cmp < 0) {
-                targetIndex = mid - 1;
-                right = mid - 1;
+            if (name.localeCompare(leafkeys[mid].key) >= 0) {
+                targetIndex = mid;
+                left = mid + 1;
             }
             else {
-                left = mid + 1;
+                right = mid - 1;
             }
         }
-        const childOffset = targetIndex >= 0 ? leafkeys[targetIndex].offset : leafkeys[0].offset;
+        const childOffset = leafkeys[Math.max(targetIndex, 0)].offset;
         return readBPlusTreeNode(bbi, childOffset, blockSize, keySize, valSize, name, field, opts);
     }
     else if (nodeType === 1) {
         // Leaf node (nodeType === 1): contains actual key-value data
         const keys = [];
         for (let i = 0; i < cnt; i++) {
-            const key = parseKey(buffer, offset, keySize);
+            const key = (0, util_ts_1.parseKey)(buffer, offset, keySize);
             offset += keySize;
             const dataOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
@@ -107,13 +94,15 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
     return undefined;
 }
 class BigBed extends bbi_ts_1.BBI {
-    readIndicesCache = new abortable_promise_cache_1.default({
-        cache: new quick_lru_1.default({ maxSize: 1 }),
-        fill: (args, signal) => this._readIndices({ ...args, signal }),
-    });
+    indicesP;
     readIndices(opts = {}) {
-        const { signal, ...rest } = opts;
-        return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
+        if (!this.indicesP) {
+            this.indicesP = this._readIndices(opts).catch((e) => {
+                this.indicesP = undefined;
+                throw e;
+            });
+        }
+        return this.indicesP;
     }
     /*
      * retrieve unzoomed view for any scale
@@ -130,8 +119,8 @@ class BigBed extends bbi_ts_1.BBI {
      */
     async _readIndices(opts) {
         const { extHeaderOffset } = await this.getHeader(opts);
-        const b = await this.bbi.read(64, extHeaderOffset);
-        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        const b = await this.bbi.read(64, extHeaderOffset, opts);
+        const dataView = (0, util_ts_1.getDataView)(b);
         const count = dataView.getUint16(2, true);
         const dataOffset = Number(dataView.getBigUint64(4, true));
         // no extra index is defined if count==0
@@ -140,11 +129,10 @@ class BigBed extends bbi_ts_1.BBI {
         }
         const blocklen = 20;
         const len = blocklen * count;
-        const buffer = await this.bbi.read(len, dataOffset);
+        const buffer = await this.bbi.read(len, dataOffset, opts);
         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);
+            const dataView = (0, util_ts_1.getDataView)(buffer, i * blocklen);
             const type = dataView.getInt16(0, true);
             const fieldcount = dataView.getInt16(2, true);
             const dataOffset = Number(dataView.getBigUint64(4, true));
@@ -176,7 +164,7 @@ class BigBed extends bbi_ts_1.BBI {
         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);
+            const dataView = (0, util_ts_1.getDataView)(b);
             const blockSize = dataView.getInt32(4, true);
             const keySize = dataView.getInt32(8, true);
             const valSize = dataView.getInt32(12, true);
@@ -211,7 +199,7 @@ class BigBed extends bbi_ts_1.BBI {
             if (!f.rest) {
                 return false;
             }
-            const fieldIndex = (f.field || 0) - 3;
+            const fieldIndex = (f.field ?? 0) - 3;
             return getTabField(f.rest, fieldIndex) === name;
         });
     }

package/dist/bigbed.js.map

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

@@ -17,7 +17,7 @@ class BigWig extends bbi_ts_1.BBI {
         const maxLevel = zoomLevels.length - 1;
         for (let i = maxLevel; i >= 0; i -= 1) {
             const zh = zoomLevels[i];
-            if (zh && zh.reductionLevel <= 2 * basesPerPx) {
+            if (zh.reductionLevel <= 2 * basesPerPx) {
                 return this.getOrCreateBlockView(refsByName, zh.indexOffset, uncompressBufSize, 'summary');
             }
         }

package/dist/bigwig.js.map

@@ -1 +1 @@
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+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;AAAA,qCAA8B;AAI9B,MAAa,MAAO,SAAQ,YAAG;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,CAAE,CAAA;YACzB,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBACxC,OAAO,IAAI,CAAC,oBAAoB,CAC9B,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,EACjB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF;AA5BD,wBA4BC"}

package/dist/block-view.d.ts

@@ -23,7 +23,7 @@ export declare class BlockView {
     private uncompressBufSize;
     private blockType;
     private rTreePromise?;
-    private featureCache;
+    private rTreeNodeCache;
     constructor(bbi: GenericFilehandle, refsByName: Record<string, number>, rTreeOffset: number, uncompressBufSize: number, blockType: string);
     private _collectBlocks;
     readWigData(chrName: string, start: number, end: number, opts?: Options): Promise<Feature[]>;