@gmod/hic 1.0.0

package/dist/hicFile.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,5 @@
+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 { Chromosome, HicMetadata, HicRegion, Reader, Zoom, } from './types.ts';

package/dist/index.js

@@ -0,0 +1,9 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readerFromFilehandle = exports.NO_DATA_FOR_RESOLUTION = exports.HicFile = void 0;
+var hicFile_ts_1 = require("./hicFile.js");
+Object.defineProperty(exports, "HicFile", { enumerable: true, get: function () { return hicFile_ts_1.HicFile; } });
+Object.defineProperty(exports, "NO_DATA_FOR_RESOLUTION", { enumerable: true, get: function () { return hicFile_ts_1.NO_DATA_FOR_RESOLUTION; } });
+var reader_ts_1 = require("./reader.js");
+Object.defineProperty(exports, "readerFromFilehandle", { enumerable: true, get: function () { return reader_ts_1.readerFromFilehandle; } });
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,2CAA8D;AAArD,qGAAA,OAAO,OAAA;AAAE,oHAAA,sBAAsB,OAAA;AACxC,yCAAkD;AAAzC,iHAAA,oBAAoB,OAAA"}

package/dist/lru.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Optional second bound, for a cache whose entries differ wildly in size.
+ *
+ * An entry cap is a memory bound only while entries are interchangeable, and the
+ * block cache's are not: a block holds every contact in its bin square, so one
+ * can be a few thousand contacts or a few hundred thousand depending on binsize
+ * and distance from the diagonal. Capping entries therefore forced one number to
+ * answer two questions — how many blocks a fetch needs at once, and how much
+ * memory the biggest of them may hold — and the memory question won, which is
+ * what left the cache too small to serve a multi-region fetch (see hicFile.ts).
+ *
+ * Splitting them lets the entry cap track the working set while `maxBytes`
+ * stays the backstop it was standing in for.
+ */
+interface WeightOpts<V> {
+    maxBytes: number;
+    weigh: (value: V) => number;
+}
+export default class LRU<K, V> {
+    private max;
+    private map;
+    private weight;
+    private weightOpts;
+    constructor(max?: number, weightOpts?: WeightOpts<V>);
+    get(key: K): V | undefined;
+    set(key: K, val: V): void;
+    delete(key: K): void;
+}
+export {};

package/dist/lru.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+class LRU {
+    max;
+    map = new Map();
+    weight = 0;
+    weightOpts;
+    constructor(max = 10, weightOpts) {
+        this.max = max;
+        this.weightOpts = weightOpts;
+    }
+    get(key) {
+        const item = this.map.get(key);
+        if (item !== undefined) {
+            // refresh key
+            this.map.delete(key);
+            this.map.set(key, item);
+        }
+        return item;
+    }
+    set(key, val) {
+        if (this.map.has(key)) {
+            // refresh key, and drop its old weight — `set` on an existing key
+            // replaces the value, so the weight it contributed goes with it
+            this.delete(key);
+        }
+        this.map.set(key, val);
+        this.weight += this.weightOpts?.weigh(val) ?? 0;
+        // Entry cap first, then the byte budget. `size > 1` keeps a single entry
+        // larger than the whole budget rather than evicting it and looping forever
+        // on an empty map — a cache that can't hold the thing just asked for should
+        // still answer the caller that asked.
+        while (this.map.size > this.max ||
+            (this.weightOpts !== undefined &&
+                this.weight > this.weightOpts.maxBytes &&
+                this.map.size > 1)) {
+            const oldest = this.map.keys().next().value;
+            if (oldest === undefined) {
+                break;
+            }
+            this.delete(oldest);
+        }
+    }
+    // Used to evict a rejected in-flight promise so the next caller retries
+    // rather than resolving against a cached failure forever.
+    delete(key) {
+        const existing = this.map.get(key);
+        if (existing !== undefined) {
+            this.weight -= this.weightOpts?.weigh(existing) ?? 0;
+        }
+        this.map.delete(key);
+    }
+}
+exports.default = LRU;
+//# sourceMappingURL=lru.js.map

package/dist/lru.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"lru.js","sourceRoot":"","sources":["../src/lru.ts"],"names":[],"mappings":";;AAmBA,MAAqB,GAAG;IACd,GAAG,CAAQ;IACX,GAAG,GAAG,IAAI,GAAG,EAAQ,CAAA;IACrB,MAAM,GAAG,CAAC,CAAA;IACV,UAAU,CAA2B;IAE7C,YAAY,GAAG,GAAG,EAAE,EAAE,UAA0B;QAC9C,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAED,GAAG,CAAC,GAAM;QACR,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,cAAc;YACd,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;YACpB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACzB,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,GAAG,CAAC,GAAM,EAAE,GAAM;QAChB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACtB,kEAAkE;YAClE,gEAAgE;YAChE,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QAE/C,yEAAyE;QACzE,2EAA2E;QAC3E,4EAA4E;QAC5E,sCAAsC;QACtC,OACE,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG;YACxB,CAAC,IAAI,CAAC,UAAU,KAAK,SAAS;gBAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ;gBACtC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,EACpB,CAAC;YACD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;YAC3C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAK;YACP,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,wEAAwE;IACxE,0DAA0D;IAC1D,MAAM,CAAC,GAAM;QACX,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAClC,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;YAC3B,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACtD,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;IACtB,CAAC;CACF;AAzDD,sBAyDC"}

package/dist/matrix.d.ts

@@ -0,0 +1,9 @@
+import MatrixZoomData from './matrixZoomData.ts';
+import type { Chromosome } from './types.ts';
+export default class Matrix {
+    private bpZoomData;
+    constructor(zoomDataList: MatrixZoomData[]);
+    getZoomData(binSize: number): MatrixZoomData | undefined;
+    static getKey(chrIdx1: number, chrIdx2: number): string;
+    static parseMatrix(data: ArrayBuffer, chromosomes: Chromosome[]): Matrix;
+}

package/dist/matrix.js

@@ -0,0 +1,41 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const binary_ts_1 = __importDefault(require("./binary.js"));
+const matrixZoomData_ts_1 = __importDefault(require("./matrixZoomData.js"));
+class Matrix {
+    // BP levels only. The FRAG code paths were dropped in this fork, so a
+    // matrix's FRAG zoom levels are parsed off the wire and discarded rather than
+    // kept in a second list nothing can reach.
+    bpZoomData;
+    constructor(zoomDataList) {
+        this.bpZoomData = zoomDataList.filter(zd => zd.zoom.unit === 'BP');
+    }
+    // Fetch zoom data by bin size. If no matching level exists return undefined.
+    getZoomData(binSize) {
+        return this.bpZoomData.find(zd => binSize === zd.zoom.binSize);
+    }
+    static getKey(chrIdx1, chrIdx2) {
+        const lo = Math.min(chrIdx1, chrIdx2);
+        const hi = Math.max(chrIdx1, chrIdx2);
+        return `${lo}_${hi}`;
+    }
+    static parseMatrix(data, chromosomes) {
+        const dis = new binary_ts_1.default(new DataView(data));
+        const c1 = dis.getInt(); // Should equal chrIdx1
+        const c2 = dis.getInt(); // Should equal chrIdx2
+        const chr1 = chromosomes[c1];
+        const chr2 = chromosomes[c2];
+        // # of resolution levels (bp and frags)
+        let nResolutions = dis.getInt();
+        const zdList = [];
+        while (nResolutions-- > 0) {
+            zdList.push(matrixZoomData_ts_1.default.parseMatrixZoomData(chr1, chr2, dis));
+        }
+        return new Matrix(zdList);
+    }
+}
+exports.default = Matrix;
+//# sourceMappingURL=matrix.js.map

package/dist/matrix.js.map

@@ -0,0 +1 @@
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package/dist/matrixZoomData.d.ts

@@ -0,0 +1,14 @@
+import type BinaryParser from './binary.ts';
+import type { BlockIndexEntry, Chromosome, HicRegion, Zoom } from './types.ts';
+export default class MatrixZoomData {
+    chr1: Chromosome;
+    chr2: Chromosome;
+    zoom: Zoom;
+    blockBinCount: number;
+    blockColumnCount: number;
+    blockIndex: Record<number, BlockIndexEntry>;
+    constructor(chr1: Chromosome, chr2: Chromosome, zoom: Zoom, 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/dist/matrixZoomData.js

@@ -0,0 +1,96 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const binWindow_ts_1 = require("./binWindow.js");
+class MatrixZoomData {
+    chr1;
+    chr2;
+    zoom;
+    blockBinCount;
+    blockColumnCount;
+    blockIndex;
+    constructor(chr1, chr2, zoom, blockBinCount, blockColumnCount, blockIndex) {
+        this.chr1 = chr1;
+        this.chr2 = chr2;
+        this.zoom = zoom;
+        this.blockBinCount = blockBinCount;
+        this.blockColumnCount = blockColumnCount;
+        this.blockIndex = blockIndex;
+    }
+    getKey() {
+        return `${this.chr1.name}_${this.chr2.name}_${this.zoom.unit}_${this.zoom.binSize}`;
+    }
+    getBlockNumbers(region1, region2, version) {
+        const sameChr = this.chr1 === this.chr2;
+        const binsize = this.zoom.binSize;
+        const blockBinCount = this.blockBinCount;
+        const blockColumnCount = this.blockColumnCount;
+        // Integer bin bounds, not the raw fractional quotients upstream used: the
+        // blocks selected here must cover every bin the record filter will accept,
+        // and `binWindow` widens that to any bin overlapping the region. Selecting
+        // too many blocks only costs a read the filter then discards; selecting too
+        // few silently drops records (see binWindow.ts).
+        const [x1, x2] = (0, binWindow_ts_1.binWindow)(region1, binsize);
+        const [y1, y2] = (0, binWindow_ts_1.binWindow)(region2, binsize);
+        // A Set dedups the block numbers that transposition can collide on the
+        // same-chr diagonal, and keeps both branches uniform.
+        const blockNumbers = new Set();
+        if (version < 9 || !sameChr) {
+            const col1 = Math.floor(x1 / blockBinCount);
+            const col2 = Math.floor((x2 - 1) / blockBinCount);
+            const row1 = Math.floor(y1 / blockBinCount);
+            const row2 = Math.floor((y2 - 1) / blockBinCount);
+            for (let row = row1; row <= row2; row++) {
+                for (let column = col1; column <= col2; column++) {
+                    blockNumbers.add(sameChr && row < column
+                        ? column * blockColumnCount + row
+                        : row * blockColumnCount + column);
+                }
+            }
+        }
+        else {
+            // PAD = positionAlongDiagonal (~projected). Depth is the axis
+            // perpendicular to the diagonal; nearer means closer to the diagonal.
+            // Widening stays safe here too: overlapping regions take the
+            // `containsDiagonal` branch (nearerDepth 0) and disjoint ones only see
+            // the near-corner gap shrink, so no depth level is lost.
+            const translatedLowerPAD = Math.floor((x1 + y1) / 2 / blockBinCount);
+            const translatedHigherPAD = Math.floor((x2 + y2) / 2 / blockBinCount);
+            const translatedNearerDepth = Math.floor(Math.log2(1 + Math.abs(x1 - y2) / Math.sqrt(2) / blockBinCount));
+            const translatedFurtherDepth = Math.floor(Math.log2(1 + Math.abs(x2 - y1) / Math.sqrt(2) / blockBinCount));
+            // code above assumes above diagonal, but we could be below it
+            const containsDiagonal = (x2 - y1) * (x1 - y2) < 0;
+            const nearerDepth = containsDiagonal
+                ? 0
+                : Math.min(translatedNearerDepth, translatedFurtherDepth);
+            const furtherDepth = Math.max(translatedNearerDepth, translatedFurtherDepth);
+            for (let depth = nearerDepth; depth <= furtherDepth; depth++) {
+                for (let pad = translatedLowerPAD; pad <= translatedHigherPAD; pad++) {
+                    blockNumbers.add(depth * blockColumnCount + pad);
+                }
+            }
+        }
+        return [...blockNumbers];
+    }
+    static parseMatrixZoomData(chr1, chr2, dis) {
+        const unit = dis.getString();
+        const zoomIndex = dis.getInt();
+        dis.getFloat(); // sumCounts
+        dis.getFloat(); // occupiedCellCount
+        dis.getFloat(); // stdDev
+        dis.getFloat(); // percent95
+        const binSize = dis.getInt();
+        const blockBinCount = dis.getInt();
+        const blockColumnCount = dis.getInt();
+        let nBlocks = dis.getInt();
+        const blockIndex = {};
+        while (nBlocks-- > 0) {
+            const blockNumber = dis.getInt();
+            const filePosition = dis.getLong();
+            const size = dis.getInt();
+            blockIndex[blockNumber] = { filePosition, size };
+        }
+        return new MatrixZoomData(chr1, chr2, { index: zoomIndex, unit, binSize }, blockBinCount, blockColumnCount, blockIndex);
+    }
+}
+exports.default = MatrixZoomData;
+//# sourceMappingURL=matrixZoomData.js.map

package/dist/matrixZoomData.js.map

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package/dist/normalizationVector.d.ts

@@ -0,0 +1,10 @@
+import type { Reader } from './types.ts';
+export default class NormalizationVector {
+    private cache;
+    private file;
+    private filePosition;
+    private nValues;
+    private dataType;
+    constructor(file: Reader, filePosition: number, nValues: number, dataType: number);
+    getValues(start: number, end: number): Promise<Float64Array<ArrayBufferLike>>;
+}

package/dist/normalizationVector.js

@@ -0,0 +1,51 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const binary_ts_1 = __importDefault(require("./binary.js"));
+const DOUBLE = 8;
+class NormalizationVector {
+    cache;
+    file;
+    filePosition;
+    nValues;
+    dataType;
+    constructor(file, filePosition, nValues, dataType) {
+        this.file = file;
+        this.filePosition = filePosition;
+        this.nValues = nValues;
+        this.dataType = dataType;
+    }
+    async getValues(start, end) {
+        // The read below clamps to `nValues`, so the cache can never cover past it.
+        // Compare against the clamped bound or a request that runs off the end of
+        // the vector — reachable when the assembly's refseq is longer than the size
+        // the `.hic` recorded for that chromosome — leaves `end > cache.end` true
+        // forever, and every call re-reads the same range from the file.
+        const wanted = Math.min(end, this.nValues);
+        if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
+            const adjustedStart = Math.max(0, start - 1000);
+            const adjustedEnd = Math.min(this.nValues, end + 1000);
+            const startPosition = this.filePosition + adjustedStart * this.dataType;
+            const n = adjustedEnd - adjustedStart;
+            const data = await this.file.read(startPosition, n * this.dataType);
+            const parser = new binary_ts_1.default(new DataView(data));
+            const values = new Float64Array(n);
+            for (let i = 0; i < n; i++) {
+                values[i] =
+                    this.dataType === DOUBLE ? parser.getDouble() : parser.getFloat();
+            }
+            this.cache = { start: adjustedStart, end: adjustedEnd, values };
+        }
+        // A view, not a copy: the caller only reads it, and a fetch asks for one of
+        // these per chromosome per region pair. Both this and `slice` clamp a
+        // request running past the end to what exists, which the caller already
+        // handles — an out-of-range index reads undefined, making the product NaN,
+        // which the record filter drops.
+        const sliceStart = start - this.cache.start;
+        return this.cache.values.subarray(sliceStart, sliceStart + (end - start));
+    }
+}
+exports.default = NormalizationVector;
+//# sourceMappingURL=normalizationVector.js.map

package/dist/normalizationVector.js.map

@@ -0,0 +1 @@
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package/dist/package.json

@@ -0,0 +1 @@
+{"type": "commonjs"}

package/dist/reader.d.ts

@@ -0,0 +1,3 @@
+import type { Reader } from './types.ts';
+import type { GenericFilehandle } from 'generic-filehandle2';
+export declare function readerFromFilehandle(filehandle: GenericFilehandle): Reader;

package/dist/reader.js

@@ -0,0 +1,12 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readerFromFilehandle = readerFromFilehandle;
+function readerFromFilehandle(filehandle) {
+    return {
+        async read(position, length) {
+            const buf = await filehandle.read(length, position);
+            return buf.buffer.slice(buf.byteOffset, buf.byteOffset + buf.byteLength);
+        },
+    };
+}
+//# sourceMappingURL=reader.js.map

package/dist/reader.js.map

@@ -0,0 +1 @@
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package/dist/types.d.ts

@@ -0,0 +1,35 @@
+/**
+ * The only read this parser needs: `length` bytes at `position`, coming back
+ * SHORT at end-of-file rather than throwing — the header walk deliberately
+ * reads past the end to discover whether a file carries normalization data at
+ * all. `generic-filehandle2` handles behave this way (a remote 416 included),
+ * and `readerFromFilehandle` adapts one to this shape.
+ */
+export interface Reader {
+    read: (position: number, length: number) => Promise<ArrayBuffer>;
+}
+export interface Chromosome {
+    index: number;
+    name: string;
+    size: number;
+}
+export interface HicRegion {
+    chr: string;
+    start: number;
+    end: number;
+}
+export interface Zoom {
+    index: number;
+    unit: string;
+    binSize: number;
+}
+export interface BlockIndexEntry {
+    filePosition: number;
+    size: number;
+}
+export interface HicMetadata {
+    version: number;
+    genome: string;
+    chromosomes: Chromosome[];
+    resolutions: number[];
+}

package/dist/types.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=types.js.map

package/dist/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":""}

package/esm/binWindow.d.ts

@@ -0,0 +1,24 @@
+import type { HicRegion } from './types.ts';
+/**
+ * Half-open `[first, last+1)` range of bin indices **overlapping** a region.
+ *
+ * Upstream hic-straw compares bin indices against the raw fractional quotients
+ * `start/binsize` and `end/binsize`, which is exact only for the
+ * chromosome-aligned queries juicebox issues. A genome browser queries
+ * arbitrary viewport windows, where `start % binsize !== 0` essentially always
+ * holds, and the raw quotient then (a) drops the bin straddling the region's
+ * start — a missing column at the left edge of every block, jittering as the
+ * user pans — while keeping the one straddling the end, and (b) selects
+ * *nothing at all* for a region narrower than one bin, which is reachable by
+ * locking a coarse binsize while zoomed in.
+ *
+ * Flooring/ceiling also matches `getNormVectors`, which already builds its
+ * vector slice over `[floor(start/binsize), ceil(end/binsize))` — so
+ * `rec.bin1 - norm.offset1` indexes exactly the values that were fetched.
+ *
+ * Lives in its own module because both the record filter (`hicFile`) and the
+ * block-number selection (`matrixZoomData`) must agree on the window: widening
+ * only one of them still drops records, since a bin can sit in a block the
+ * other never asked for.
+ */
+export declare function binWindow(region: HicRegion, binsize: number): readonly [number, number];

package/esm/binWindow.js

@@ -0,0 +1,29 @@
+/**
+ * Half-open `[first, last+1)` range of bin indices **overlapping** a region.
+ *
+ * Upstream hic-straw compares bin indices against the raw fractional quotients
+ * `start/binsize` and `end/binsize`, which is exact only for the
+ * chromosome-aligned queries juicebox issues. A genome browser queries
+ * arbitrary viewport windows, where `start % binsize !== 0` essentially always
+ * holds, and the raw quotient then (a) drops the bin straddling the region's
+ * start — a missing column at the left edge of every block, jittering as the
+ * user pans — while keeping the one straddling the end, and (b) selects
+ * *nothing at all* for a region narrower than one bin, which is reachable by
+ * locking a coarse binsize while zoomed in.
+ *
+ * Flooring/ceiling also matches `getNormVectors`, which already builds its
+ * vector slice over `[floor(start/binsize), ceil(end/binsize))` — so
+ * `rec.bin1 - norm.offset1` indexes exactly the values that were fetched.
+ *
+ * Lives in its own module because both the record filter (`hicFile`) and the
+ * block-number selection (`matrixZoomData`) must agree on the window: widening
+ * only one of them still drops records, since a bin can sit in a block the
+ * other never asked for.
+ */
+export function binWindow(region, binsize) {
+    return [
+        Math.floor(region.start / binsize),
+        Math.ceil(region.end / binsize),
+    ];
+}
+//# sourceMappingURL=binWindow.js.map

package/esm/binWindow.js.map

@@ -0,0 +1 @@
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package/esm/binary.d.ts

@@ -0,0 +1,15 @@
+export default class BinaryParser {
+    position: number;
+    private view;
+    private length;
+    private littleEndian;
+    constructor(dataView: DataView, littleEndian?: boolean);
+    available(): number;
+    getByte(): number;
+    getShort(): number;
+    getInt(): number;
+    getLong(): number;
+    getString(): string;
+    getFloat(): number;
+    getDouble(): number;
+}

package/esm/binary.js

@@ -0,0 +1,64 @@
+export default class BinaryParser {
+    position = 0;
+    view;
+    length;
+    littleEndian;
+    constructor(dataView, littleEndian = true) {
+        this.view = dataView;
+        this.length = dataView.byteLength;
+        this.littleEndian = littleEndian;
+    }
+    available() {
+        return this.length - this.position;
+    }
+    getByte() {
+        const ret = this.view.getUint8(this.position);
+        this.position += 1;
+        return ret;
+    }
+    getShort() {
+        const ret = this.view.getInt16(this.position, this.littleEndian);
+        this.position += 2;
+        return ret;
+    }
+    getInt() {
+        const ret = this.view.getInt32(this.position, this.littleEndian);
+        this.position += 4;
+        return ret;
+    }
+    // No native 64-bit read that lands in a `number`, so compose two 32-bit words
+    // (deliberately not getBigUint64 — every caller is a file offset or a count
+    // that stays well inside Number.MAX_SAFE_INTEGER, and a BigInt would have to
+    // be converted back at each use site). hic-straw accumulated byte-by-byte
+    // through a throwaway 8-element array, which is a per-entry allocation in the
+    // block-index parse loop.
+    getLong() {
+        const p = this.position;
+        const le = this.littleEndian;
+        const first = this.view.getUint32(p, le);
+        const second = this.view.getUint32(p + 4, le);
+        this.position += 8;
+        // little-endian puts the low word first, big-endian the high word
+        return le ? second * 0x1_0000_0000 + first : first * 0x1_0000_0000 + second;
+    }
+    getString() {
+        let s = '';
+        let c = this.view.getUint8(this.position++);
+        while (c !== 0) {
+            s += String.fromCharCode(c);
+            c = this.view.getUint8(this.position++);
+        }
+        return s;
+    }
+    getFloat() {
+        const ret = this.view.getFloat32(this.position, this.littleEndian);
+        this.position += 4;
+        return ret;
+    }
+    getDouble() {
+        const ret = this.view.getFloat64(this.position, this.littleEndian);
+        this.position += 8;
+        return ret;
+    }
+}
+//# sourceMappingURL=binary.js.map