@gmod/hic 2.0.0 → 2.2.0

package/esm/hicFile.d.ts

@@ -2,7 +2,7 @@ import Matrix from './matrix.ts';
 import NormalizationVector from './normalizationVector.ts';
 import type { ContactRecords } from './contactRecords.ts';
 import type MatrixZoomData from './matrixZoomData.ts';
-import type { BaseOpts, BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
+import type { BaseOpts, BlockIndexEntry, ExpectedValues, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 /**
  * Prefix of the error thrown when a region pair has no matrix at the requested
@@ -40,6 +40,7 @@ export declare class HicFile {
     private file;
     private headerCache;
     private normVectorIndexCache;
+    private expectedSectionCache;
     private normVectorCache;
     private matrixCache;
     private blockCache;
@@ -48,6 +49,7 @@ export declare class HicFile {
     private version;
     private genomeId;
     private footerPosition;
+    private expectedValuesPosition;
     normExpectedValueVectorsPosition: number | undefined;
     private chromosomes;
     private chromosomeIndexMap;
@@ -87,7 +89,27 @@ export declare class HicFile {
     getNormalizationOptions(opts?: ProgressOpts): Promise<string[]>;
     private readNormVectorIndex;
     private readNormExpectedValuesAndNormVectorIndex;
-    private skipExpectedValues;
+    /**
+     * The expected count for a region pair at `binsize`, the denominator of
+     * observed/expected, as straw computes it. `normalization` must be the one
+     * the pair's records carry (`getContactRecords`' `appliedNormalization`),
+     * since each normalization has its own vector. Undefined where the file has
+     * no expected value for it: no vector at this binsize, or a version 5 file
+     * asked for a normalized one.
+     *
+     * Within a chromosome the vector is read for only the distances the pair
+     * spans. Between chromosomes straw divides by the map's average contact, the
+     * raw `sumCounts` over its bins, whatever the normalization.
+     */
+    getExpectedValues(normalization: string, region1: HicRegion, region2: HicRegion, binsize: number, opts?: ProgressOpts): Promise<ExpectedValues | undefined>;
+    /**
+     * The library's total contact count, the `ALL` whole-genome map's
+     * `sumCounts`: what scales two libraries of different depth against each
+     * other. Undefined for a file with no `ALL` map.
+     */
+    getTotalContacts(opts?: BaseOpts): Promise<number | undefined>;
+    private getExpectedSection;
+    private walkExpectedSection;
     private parseNormVectorEntry;
 }
 export {};

package/esm/hicFile.js

@@ -18,6 +18,18 @@ const Short_MIN_VALUE = -32768;
 const DOUBLE = 8;
 const FLOAT = 4;
 const INT = 4;
+function getExpectedKey(type, unit, binSize) {
+    return `${type}_${unit}_${binSize}`;
+}
+// The range of `|bin2 - bin1|` over two half-open bin windows.
+function distanceRange([x1, x2], [y1, y2]) {
+    const overlap = x1 < y2 && y1 < x2;
+    const nearest = overlap
+        ? 0
+        : Math.min(Math.abs(y1 - (x2 - 1)), Math.abs(x1 - (y2 - 1)));
+    const farthest = Math.max(Math.abs(y2 - 1 - x1), Math.abs(x2 - 1 - y1));
+    return [nearest, farthest];
+}
 /**
  * Copy a partially-filled decode buffer down to its true length, or hand it
  * back untouched when the filter dropped nothing. A `subarray` would be free
@@ -106,6 +118,9 @@ export class HicFile {
     // it has aborted, and drops a rejection so the next caller retries.
     headerCache = new SharedReadCache();
     normVectorIndexCache = new SharedReadCache();
+    // 'raw' and 'normalized', each walked once: the sections carry no index, so
+    // a chunk's position is known only by walking every chunk before it.
+    expectedSectionCache = new SharedReadCache();
     normVectorCache = new SharedReadCache({ maxSize: NORM_VECTOR_CACHE_SIZE });
     matrixCache = new SharedReadCache({
         maxSize: MATRIX_CACHE_SIZE,
@@ -118,6 +133,8 @@ export class HicFile {
     version = 0;
     genomeId = '';
     footerPosition = 0;
+    // Where the raw (NONE) expected values begin, right after the master index.
+    expectedValuesPosition = 0;
     // Where the file's normalization data begins, and so also where a file
     // carrying none of it ends. Public so a test can cut a real file there to
     // make that second shape.
@@ -170,7 +187,7 @@ export class HicFile {
             throw new Error(`Unsupported hic version: ${version}`);
         }
         const footerPosition = binaryParser.getLong();
-        const { masterIndex, normExpectedValueVectorsPosition } = await this.readFooter(version, footerPosition, signal);
+        const { masterIndex, expectedValuesPosition, normExpectedValueVectorsPosition, } = await this.readFooter(version, footerPosition, signal);
         const bodyPosition = Object.values(masterIndex).reduce((min, entry) => Math.min(min, entry.start), Number.MAX_VALUE);
         data = await this.file.read(16, bodyPosition - 16, { signal });
         binaryParser = new BinaryParser(new DataView(data));
@@ -208,6 +225,7 @@ export class HicFile {
         throwIfAborted(signal);
         this.version = version;
         this.footerPosition = footerPosition;
+        this.expectedValuesPosition = expectedValuesPosition;
         this.masterIndex = masterIndex;
         this.normExpectedValueVectorsPosition = normExpectedValueVectorsPosition;
         this.genomeId = genomeId;
@@ -242,9 +260,14 @@ export class HicFile {
             const size = binaryParser.getInt();
             masterIndex[key] = { start: pos, size };
         }
+        const expectedValuesPosition = footerPosition + skip + binaryParser.position;
         // Normalized expected values start after the expected values
         const normExpectedValueVectorsPosition = version > 5 ? footerPosition + (version < 9 ? 4 : 8) + nBytes : undefined;
-        return { masterIndex, normExpectedValueVectorsPosition };
+        return {
+            masterIndex,
+            expectedValuesPosition,
+            normExpectedValueVectorsPosition,
+        };
     }
     async getMatrix(chrIdx1, chrIdx2, opts) {
         await this.init(opts);
@@ -672,7 +695,7 @@ export class HicFile {
         const { signal } = opts;
         let index;
         if (this.normExpectedValueVectorsPosition !== undefined) {
-            const nviStart = await this.skipExpectedValues(this.normExpectedValueVectorsPosition, opts);
+            const nviStart = (await this.getExpectedSection('normalized', opts)).end;
             const data = await this.file.read(nviStart, INT, { signal });
             // Possible if there are no norm vectors. A legal v8 file, though uncommon.
             if (data.byteLength !== 0) {
@@ -699,64 +722,135 @@ export class HicFile {
         }
         return index;
     }
-    // Used when the position of the norm vector index is unknown: skip the
-    // normalized expected values to find the index.
-    async skipExpectedValues(start, opts) {
+    /**
+     * The expected count for a region pair at `binsize`, the denominator of
+     * observed/expected, as straw computes it. `normalization` must be the one
+     * the pair's records carry (`getContactRecords`' `appliedNormalization`),
+     * since each normalization has its own vector. Undefined where the file has
+     * no expected value for it: no vector at this binsize, or a version 5 file
+     * asked for a normalized one.
+     *
+     * Within a chromosome the vector is read for only the distances the pair
+     * spans. Between chromosomes straw divides by the map's average contact, the
+     * raw `sumCounts` over its bins, whatever the normalization.
+     */
+    async getExpectedValues(normalization, region1, region2, binsize, opts) {
+        await this.init(opts);
+        const idx1 = this.chromosomeIndexMap.get(region1.chr);
+        const idx2 = this.chromosomeIndexMap.get(region2.chr);
+        if (idx1 === undefined || idx2 === undefined) {
+            return undefined;
+        }
+        if (idx1 !== idx2) {
+            const matrix = await this.getMatrix(idx1, idx2, opts);
+            const zd = matrix?.getZoomData(binsize);
+            if (!zd) {
+                return undefined;
+            }
+            // straw's bin counts leave out a chromosome's partial last bin
+            const nBins1 = Math.max(1, Math.floor(this.chromosomes[idx1].size / binsize));
+            const nBins2 = Math.max(1, Math.floor(this.chromosomes[idx2].size / binsize));
+            return { kind: 'inter', average: zd.sumCounts / nBins1 / nBins2 };
+        }
+        const normalized = !!normalization && normalization !== 'NONE';
+        if (normalized && this.normExpectedValueVectorsPosition === undefined) {
+            return undefined;
+        }
+        const section = await this.getExpectedSection(normalized ? 'normalized' : 'raw', opts ?? {});
+        const chunk = section.chunks.get(getExpectedKey(normalized ? normalization : 'NONE', 'BP', binsize));
+        if (!chunk || chunk.nValues === 0) {
+            return undefined;
+        }
+        const [first, last] = distanceRange(binWindow(region1, binsize), binWindow(region2, binsize));
+        const signalOpts = { signal: opts?.signal };
+        const stored = await chunk.vector.getValues(first, last + 1, signalOpts);
+        const tail = stored.length < last + 1 - first
+            ? (await chunk.vector.getValues(chunk.nValues - 1, chunk.nValues, signalOpts))[0]
+            : 0;
+        // straw divides by 1 where the section names no factor for the chromosome
+        const factor = chunk.chrScaleFactors.get(idx1) ?? 1;
+        const values = new Float64Array(last + 1 - first);
+        for (let i = 0; i < values.length; i++) {
+            values[i] = (i < stored.length ? stored[i] : tail) / factor;
+        }
+        return { kind: 'intra', firstDistance: first, values };
+    }
+    /**
+     * The library's total contact count, the `ALL` whole-genome map's
+     * `sumCounts`: what scales two libraries of different depth against each
+     * other. Undefined for a file with no `ALL` map.
+     */
+    async getTotalContacts(opts) {
+        await this.init(opts);
+        const all = this.chromosomes.find(chr => chr.name.toUpperCase() === 'ALL');
+        const zd = all
+            ? (await this.getMatrix(all.index, all.index, opts))?.getZoomLevels()[0]
+            : undefined;
+        return zd?.sumCounts;
+    }
+    async getExpectedSection(section, opts) {
+        return this.expectedSectionCache.get(section, opts.signal, signal => this.walkExpectedSection(section === 'raw'
+            ? this.expectedValuesPosition
+            : this.normExpectedValueVectorsPosition, section === 'normalized', { signal, onProgress: opts.onProgress }));
+    }
+    // Walk one expected-value section, recording where each chunk's values sit
+    // and its chromosome scale factors. The normalized section's end is also
+    // where a pre-v9 file's normalization vector index begins.
+    //
+    // A chunk's two reads land a whole expected-value vector apart — one per bin
+    // of the genome's longest chromosome, so megabytes at a fine binsize — which
+    // is further than the buffer reaches. On a remote file that is two round
+    // trips per chunk that nothing can merge, and it is why this walk, not the
+    // index it leads to, is the slow part of opening a pre-v9 file. It is also
+    // why the chunk is the unit worth counting: known before the first read, each
+    // costing about the same. Chunks are walked in order, since each one's size
+    // is known only once the one before it has been parsed.
+    async walkExpectedSection(start, normalized, opts) {
         const { signal, onProgress } = opts;
         const version = this.version;
+        const valueSize = version < 9 ? DOUBLE : FLOAT;
         const file = new BufferedFile({ file: this.file, size: 256000 });
+        const chunks = new Map();
         const data = await file.read(start, INT, { signal });
-        // A file with no normalization at all ends where this section would start,
-        // so the count this is about to read is past EOF. That is the same "no norm
-        // vectors" case `readNormExpectedValuesAndNormVectorIndex` guards its own
-        // read for, and it has to be caught HERE too, because this runs first:
-        // a v9 file that records no norm-vector-index position takes the v8
-        // discovery path, and that path starts by skipping a section that isn't
-        // there. Answering `start` leaves the caller's guard to do the rest.
+        // A file with no normalization at all ends where the normalized section
+        // would start, so the count this is about to read is past EOF. A v9 file
+        // that records no norm-vector-index position takes the v8 discovery path,
+        // which starts by walking a section that isn't there, so the empty answer
+        // has to come from here.
         if (data.byteLength < INT) {
-            return start;
+            return { chunks, end: start };
         }
-        const binaryParser = new BinaryParser(new DataView(data));
-        const nEntries = binaryParser.getInt(); // Total # of expected value chunks
-        // Skip one chunk, answering where the next one starts.
-        //
-        // Its two reads land a whole expected-value vector apart — one per bin of
-        // the genome, so tens of MB at a fine binsize — which is further than the
-        // buffer reaches. On a remote file that is two round trips per chunk that
-        // nothing can merge, and it is why this walk, not the index it is looking
-        // for, is the slow part of opening a pre-v9 file. It is also why the chunk
-        // is the unit worth counting: `nEntries` of them, known before the first
-        // read, each costing about the same.
-        const skipChunk = async (chunkStart) => {
-            let chunkSize = 0;
-            let buf = await file.read(chunkStart, 500, { signal });
-            let parser = new BinaryParser(new DataView(buf));
-            parser.getString(); // type
-            parser.getString(); // unit
-            parser.getInt(); // binSize
-            const nValues = version < 9 ? parser.getInt() : parser.getLong();
-            chunkSize += parser.position + nValues * (version < 9 ? DOUBLE : FLOAT);
-            buf = await file.read(chunkStart + chunkSize, INT, { signal });
-            parser = new BinaryParser(new DataView(buf));
-            const nChrScaleFactors = parser.getInt();
-            chunkSize +=
-                INT + nChrScaleFactors * (INT + (version < 9 ? DOUBLE : FLOAT));
-            return chunkStart + chunkSize;
-        };
-        // A loop rather than the tail recursion this was, because the position is
-        // the only thing carried between chunks and a counter now rides along with
-        // it. Chunks must be walked in order — each one's size is only known once
-        // the one before it has been parsed — so the awaits are sequential by
-        // nature, not by oversight.
+        const nEntries = new BinaryParser(new DataView(data)).getInt();
         if (nEntries > 0) {
             onProgress?.(0, nEntries);
         }
         let position = start + INT;
         for (let done = 0; done < nEntries; done++) {
-            position = await skipChunk(position);
+            let parser = new BinaryParser(new DataView(await file.read(position, 500, { signal })));
+            const type = normalized ? parser.getString() : 'NONE';
+            const unit = parser.getString();
+            const binSize = parser.getInt();
+            const nValues = version < 9 ? parser.getInt() : parser.getLong();
+            const valuesPosition = position + parser.position;
+            const factorsPosition = valuesPosition + nValues * valueSize;
+            parser = new BinaryParser(new DataView(await file.read(factorsPosition, INT, { signal })));
+            const nFactors = parser.getInt();
+            const factorBytes = nFactors * (INT + valueSize);
+            parser = new BinaryParser(new DataView(await file.read(factorsPosition + INT, factorBytes, { signal })));
+            const chrScaleFactors = new Map();
+            for (let i = 0; i < nFactors; i++) {
+                const chrIdx = parser.getInt();
+                chrScaleFactors.set(chrIdx, version < 9 ? parser.getDouble() : parser.getFloat());
+            }
+            chunks.set(getExpectedKey(type, unit, binSize), {
+                vector: new NormalizationVector(this.file, valuesPosition, nValues, valueSize),
+                nValues,
+                chrScaleFactors,
+            });
+            position = factorsPosition + INT + factorBytes;
             onProgress?.(done + 1, nEntries);
         }
-        return position;
+        return { chunks, end: position };
     }
     parseNormVectorEntry(binaryParser, index) {
         const type = binaryParser.getString(); // 15

package/esm/hicFile.js.map

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

@@ -2,4 +2,4 @@ export { HicFile, NO_DATA_FOR_RESOLUTION } from './hicFile.ts';
 export { readerFromFilehandle } from './reader.ts';
 export type { HicConfig } from './hicFile.ts';
 export type { ContactRecords } from './contactRecords.ts';
-export type { BaseOpts, Chromosome, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';
+export type { BaseOpts, Chromosome, ExpectedValues, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';

package/esm/matrix.d.ts

@@ -3,6 +3,8 @@ import type { Chromosome } from './types.ts';
 export default class Matrix {
     private bpZoomData;
     constructor(zoomDataList: MatrixZoomData[]);
+    /** The BP zoom levels this matrix holds, finest last as the file lists them. */
+    getZoomLevels(): readonly MatrixZoomData[];
     getZoomData(binSize: number): MatrixZoomData | undefined;
     static getKey(chrIdx1: number, chrIdx2: number): string;
     static parseMatrix(data: ArrayBuffer, chromosomes: Chromosome[]): Matrix;

package/esm/matrix.js

@@ -8,6 +8,10 @@ export default class Matrix {
     constructor(zoomDataList) {
         this.bpZoomData = zoomDataList.filter(zd => zd.zoom.unit === 'BP');
     }
+    /** The BP zoom levels this matrix holds, finest last as the file lists them. */
+    getZoomLevels() {
+        return this.bpZoomData;
+    }
     // Fetch zoom data by bin size. If no matching level exists return undefined.
     getZoomData(binSize) {
         return this.bpZoomData.find(zd => binSize === zd.zoom.binSize);

package/esm/matrix.js.map

@@ -1 +1 @@
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+{"version":3,"file":"matrix.js","sourceRoot":"","sources":["../src/matrix.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,aAAa,CAAA;AACtC,OAAO,cAAc,MAAM,qBAAqB,CAAA;AAIhD,MAAM,CAAC,OAAO,OAAO,MAAM;IACzB,sEAAsE;IACtE,8EAA8E;IAC9E,2CAA2C;IACnC,UAAU,CAAkB;IAEpC,YAAY,YAA8B;QACxC,IAAI,CAAC,UAAU,GAAG,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,CAAA;IACpE,CAAC;IAED,gFAAgF;IAChF,aAAa;QACX,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,6EAA6E;IAC7E,WAAW,CAAC,OAAe;QACzB,OAAO,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAChE,CAAC;IAED,MAAM,CAAC,MAAM,CAAC,OAAe,EAAE,OAAe;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACrC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACrC,OAAO,GAAG,EAAE,IAAI,EAAE,EAAE,CAAA;IACtB,CAAC;IAED,MAAM,CAAC,WAAW,CAAC,IAAiB,EAAE,WAAyB;QAC7D,MAAM,GAAG,GAAG,IAAI,YAAY,CAAC,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;QAChD,MAAM,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA,CAAC,uBAAuB;QAC/C,MAAM,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA,CAAC,uBAAuB;QAE/C,MAAM,IAAI,GAAG,WAAW,CAAC,EAAE,CAAE,CAAA;QAC7B,MAAM,IAAI,GAAG,WAAW,CAAC,EAAE,CAAE,CAAA;QAE7B,wCAAwC;QACxC,IAAI,YAAY,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA;QAC/B,MAAM,MAAM,GAAqB,EAAE,CAAA;QACnC,OAAO,YAAY,EAAE,GAAG,CAAC,EAAE,CAAC;YAC1B,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,mBAAmB,CAAC,IAAI,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;QAClE,CAAC;QACD,OAAO,IAAI,MAAM,CAAC,MAAM,CAAC,CAAA;IAC3B,CAAC;CACF"}

package/esm/matrixZoomData.d.ts

@@ -4,10 +4,12 @@ export default class MatrixZoomData {
     chr1: Chromosome;
     chr2: Chromosome;
     zoom: Zoom;
+    /** the raw contacts summed over the whole map at this binsize */
+    sumCounts: number;
     blockBinCount: number;
     blockColumnCount: number;
     blockIndex: Record<number, BlockIndexEntry>;
-    constructor(chr1: Chromosome, chr2: Chromosome, zoom: Zoom, blockBinCount: number, blockColumnCount: number, blockIndex: Record<number, BlockIndexEntry>);
+    constructor(chr1: Chromosome, chr2: Chromosome, zoom: Zoom, sumCounts: number, blockBinCount: number, blockColumnCount: number, blockIndex: Record<number, BlockIndexEntry>);
     getKey(): string;
     getBlockNumbers(region1: HicRegion, region2: HicRegion, version: number): number[];
     static parseMatrixZoomData(chr1: Chromosome, chr2: Chromosome, dis: BinaryParser): MatrixZoomData;

package/esm/matrixZoomData.js

@@ -3,13 +3,16 @@ export default class MatrixZoomData {
     chr1;
     chr2;
     zoom;
+    /** the raw contacts summed over the whole map at this binsize */
+    sumCounts;
     blockBinCount;
     blockColumnCount;
     blockIndex;
-    constructor(chr1, chr2, zoom, blockBinCount, blockColumnCount, blockIndex) {
+    constructor(chr1, chr2, zoom, sumCounts, blockBinCount, blockColumnCount, blockIndex) {
         this.chr1 = chr1;
         this.chr2 = chr2;
         this.zoom = zoom;
+        this.sumCounts = sumCounts;
         this.blockBinCount = blockBinCount;
         this.blockColumnCount = blockColumnCount;
         this.blockIndex = blockIndex;
@@ -72,7 +75,7 @@ export default class MatrixZoomData {
     static parseMatrixZoomData(chr1, chr2, dis) {
         const unit = dis.getString();
         const zoomIndex = dis.getInt();
-        dis.getFloat(); // sumCounts
+        const sumCounts = dis.getFloat();
         dis.getFloat(); // occupiedCellCount
         dis.getFloat(); // stdDev
         dis.getFloat(); // percent95
@@ -87,7 +90,7 @@ export default class MatrixZoomData {
             const size = dis.getInt();
             blockIndex[blockNumber] = { filePosition, size };
         }
-        return new MatrixZoomData(chr1, chr2, { index: zoomIndex, unit, binSize }, blockBinCount, blockColumnCount, blockIndex);
+        return new MatrixZoomData(chr1, chr2, { index: zoomIndex, unit, binSize }, sumCounts, blockBinCount, blockColumnCount, blockIndex);
     }
 }
 //# sourceMappingURL=matrixZoomData.js.map

package/esm/matrixZoomData.js.map

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

@@ -56,6 +56,22 @@ export interface BlockIndexEntry {
     filePosition: number;
     size: number;
 }
+/**
+ * The expected contact count for one region pair, the denominator of
+ * observed/expected. Within a chromosome it depends only on the distance in
+ * bins, so it is the expected-value vector's entries over the distances the
+ * pair spans: `values[|bin2 - bin1| - firstDistance]`, already divided by the
+ * chromosome's scale factor and holding the vector's last value past its end.
+ * Between chromosomes it is one number, the map's average contact.
+ */
+export type ExpectedValues = {
+    kind: 'intra';
+    firstDistance: number;
+    values: Float64Array;
+} | {
+    kind: 'inter';
+    average: number;
+};
 export interface HicMetadata {
     version: number;
     genome: string;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/hic",
-  "version": "2.0.0",
+  "version": "2.2.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Read .hic contact matrix files in node or the browser",
   "license": "MIT",