@jbrowse/plugin-hic 3.6.5 → 4.0.0

package/esm/HicAdapter/HicAdapter.d.ts

@@ -4,6 +4,13 @@ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import type { Region } from '@jbrowse/core/util/types';
+export interface MultiRegionContactRecord {
+    bin1: number;
+    bin2: number;
+    counts: number;
+    region1Idx: number;
+    region2Idx: number;
+}
 interface HicOptions extends BaseOptions {
     resolution?: number;
     bpPerPx?: number;
@@ -15,11 +22,13 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
     private setup;
     getHeader(opts?: BaseOptions): Promise<{
         norms: any;
+        hasInterChromosomalData: boolean;
         resolutions: number[];
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getResolution(res: number, opts?: BaseOptions): Promise<number>;
     getFeatures(region: Region, opts?: HicOptions): any;
+    getMultiRegionContactRecords(regions: Region[], opts?: HicOptions): Promise<MultiRegionContactRecord[]>;
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;

package/esm/HicAdapter/HicAdapter.js

@@ -2,8 +2,9 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import HicStraw from 'hic-straw';
-import { openHicFilehandle } from './HicFilehandle';
+import { openHicFilehandle } from "./HicFilehandle.js";
 export default class HicAdapter extends BaseFeatureDataAdapter {
+    hic;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.hic = new HicStraw({
@@ -17,7 +18,13 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
     async getHeader(opts) {
         const { chromosomes, ...rest } = await this.setup(opts);
         const norms = await this.hic.getNormalizationOptions();
-        return { ...rest, norms };
+        await this.hic.hicFile.init();
+        const { masterIndex } = this.hic.hicFile;
+        const hasInterChromosomalData = Object.keys(masterIndex).some(key => {
+            const [idx1, idx2] = key.split('_');
+            return idx1 !== idx2;
+        });
+        return { ...rest, norms, hasInterChromosomalData };
     }
     async getRefNames(opts) {
         const metadata = await this.setup(opts);
@@ -49,6 +56,30 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
+    async getMultiRegionContactRecords(regions, opts = {}) {
+        const { resolution, normalization = 'KR', bpPerPx = 1, statusCallback = () => { }, } = opts;
+        const res = await this.getResolution(bpPerPx / (resolution || 1000), opts);
+        const allRecords = [];
+        await updateStatus('Downloading .hic data', statusCallback, async () => {
+            for (let i = 0; i < regions.length; i++) {
+                for (let j = i; j < regions.length; j++) {
+                    const region1 = regions[i];
+                    const region2 = regions[j];
+                    const records = await this.hic.getContactRecords(normalization, { chr: region1.refName, start: region1.start, end: region1.end }, { chr: region2.refName, start: region2.start, end: region2.end }, 'BP', res);
+                    for (const { bin1, bin2, counts } of records) {
+                        allRecords.push({
+                            bin1,
+                            bin2,
+                            counts,
+                            region1Idx: i,
+                            region2Idx: j,
+                        });
+                    }
+                }
+            }
+        });
+        return allRecords;
+    }
     async getMultiRegionFeatureDensityStats(_regions) {
         return {
             featureDensity: 0,

package/esm/HicAdapter/HicFilehandle.js

@@ -1,5 +1,6 @@
 import { openLocation } from '@jbrowse/core/util/io';
 class HicFilehandle {
+    filehandle;
     constructor(filehandle) {
         this.filehandle = filehandle;
     }

package/esm/HicAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const HicAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     hicLocation: {
         type: string;
         defaultValue: {
@@ -11,5 +11,5 @@ declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchem
         defaultValue: number;
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HicAdapter;

package/esm/HicAdapter/index.js

@@ -1,10 +1,10 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function HicAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'HicAdapter',
         displayName: 'Hi-C adapter',
         configSchema,
-        getAdapterClass: () => import('./HicAdapter').then(r => r.default),
+        getAdapterClass: () => import("./HicAdapter.js").then(r => r.default),
     }));
 }

package/esm/HicRenderer/HicRenderer.d.ts

@@ -1,54 +1,25 @@
 import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { MultiRegionContactRecord } from '../HicAdapter/HicAdapter.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { RenderArgs as ServerSideRenderArgs, RenderArgsDeserialized as ServerSideRenderArgsDeserialized, ResultsDeserialized as ServerSideResultsDeserialized, ResultsSerialized as ServerSideResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { RenderArgsDeserialized as ServerSideRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
 import type { Region } from '@jbrowse/core/util/types';
-interface HicFeature {
-    bin1: number;
-    bin2: number;
-    counts: number;
-}
-interface HicDataAdapter extends BaseFeatureDataAdapter {
-    getResolution: (bp: number) => Promise<number>;
-}
-export interface RenderArgs extends ServerSideRenderArgs {
-    regions: Region[];
-}
+export type HicFeature = MultiRegionContactRecord;
 export interface RenderArgsDeserialized extends ServerSideRenderArgsDeserialized {
     regions: Region[];
-    dataAdapter: HicDataAdapter;
     bpPerPx: number;
     highResolutionScaling: number;
     resolution: number;
     adapterConfig: AnyConfigurationModel;
     displayHeight?: number;
+    useLogScale?: boolean;
+    colorScheme?: string;
 }
 export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
     features: HicFeature[];
     statusCallback?: (arg: string) => void;
 }
-export type ResultsSerialized = ServerSideResultsSerialized;
-export type ResultsDeserialized = ServerSideResultsDeserialized;
 export default class HicRenderer extends ServerSideRendererType {
     supportsSVG: boolean;
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        height: number;
-        width: number;
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        height: number;
-        width: number;
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        height: number;
-        width: number;
-        reactElement: React.ReactElement;
-        html?: string;
-    }>;
-    getFeatures(args: RenderArgsDeserialized): Promise<any>;
+    render(renderProps: RenderArgsDeserialized): Promise<import("librpc-web-mod").RpcResult>;
+    getFeatures(args: RenderArgsDeserialized): Promise<MultiRegionContactRecord[]>;
 }
-export type { RenderArgsSerialized, RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';

package/esm/HicRenderer/HicRenderer.js

@@ -1,48 +1,41 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import { rpcResult } from '@jbrowse/core/util/librpc';
+import { collectTransferables } from '@jbrowse/core/util/offscreenCanvasPonyfill';
 import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils';
-import { firstValueFrom } from 'rxjs';
-import { toArray } from 'rxjs/operators';
 export default class HicRenderer extends ServerSideRendererType {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
+    supportsSVG = true;
     async render(renderProps) {
-        const { displayHeight, regions, bpPerPx } = renderProps;
-        const region = regions[0];
-        const width = (region.end - region.start) / bpPerPx;
+        const { displayHeight, regions, bpPerPx, colorScheme, useLogScale } = renderProps;
+        let totalWidthBp = 0;
+        for (const region of regions) {
+            totalWidthBp += region.end - region.start;
+        }
+        const width = totalWidthBp / bpPerPx;
         const hyp = width / 2;
-        const height = displayHeight !== null && displayHeight !== void 0 ? displayHeight : hyp;
+        const height = displayHeight ?? hyp;
         const features = await this.getFeatures(renderProps);
-        const { makeImageData } = await import('./makeImageData');
+        const yScalar = height / Math.max(height, hyp);
+        const { makeImageData } = await import("./makeImageData.js");
         const res = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData(ctx, {
             ...renderProps,
-            yScalar: height / Math.max(height, hyp),
+            yScalar,
             features,
             pluginManager: this.pluginManager,
         }));
-        const results = await super.render({
-            ...renderProps,
-            ...res,
-            features,
-            region: renderProps.regions[0],
-            height,
-            width,
-        });
-        return {
-            ...results,
+        const serialized = {
             ...res,
             height,
             width,
+            yScalar,
+            colorScheme,
+            useLogScale,
         };
+        return rpcResult(serialized, collectTransferables(serialized));
     }
     async getFeatures(args) {
         const { regions, sessionId, adapterConfig } = args;
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
-        const features = await firstValueFrom(dataAdapter
-            .getFeatures(regions[0], args)
-            .pipe(toArray()));
-        return features;
+        return dataAdapter.getMultiRegionContactRecords(regions, args);
     }
 }

package/esm/HicRenderer/components/HicColorLegend.d.ts

@@ -0,0 +1,6 @@
+declare const HicColorLegend: ({ maxScore, colorScheme, useLogScale, }: {
+    maxScore: number;
+    colorScheme?: string;
+    useLogScale?: boolean;
+}) => import("react/jsx-runtime").JSX.Element;
+export default HicColorLegend;

package/esm/HicRenderer/components/HicColorLegend.js

@@ -0,0 +1,52 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { toLocale } from '@jbrowse/core/util';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { scaleLinear, scaleLog } from '@mui/x-charts-vendor/d3-scale';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()({
+    legend: {
+        position: 'absolute',
+        right: 10,
+        top: 10,
+        background: 'rgba(255,255,255,0.9)',
+        border: '1px solid #ccc',
+        borderRadius: 4,
+        padding: 8,
+        fontSize: 11,
+        pointerEvents: 'none',
+        zIndex: 100,
+    },
+    gradientBar: {
+        width: 100,
+        height: 12,
+        marginBottom: 4,
+        borderRadius: 2,
+    },
+    labels: {
+        display: 'flex',
+        justifyContent: 'space-between',
+        fontSize: 10,
+    },
+});
+const colorGradients = {
+    juicebox: 'linear-gradient(to right, rgba(0,0,0,0), red)',
+    fall: 'linear-gradient(to right, rgb(255,255,255), rgb(255,255,204), rgb(255,237,160), rgb(254,217,118), rgb(254,178,76), rgb(253,141,60), rgb(252,78,42), rgb(227,26,28), rgb(189,0,38), rgb(128,0,38), rgb(0,0,0))',
+    viridis: 'linear-gradient(to right, #440154, #482878, #3e4a89, #31688e, #26828e, #1f9e89, #35b779, #6ece58, #b5de2b, #fde725)',
+};
+function getNiceScale(maxScore, useLogScale) {
+    if (useLogScale) {
+        const scale = scaleLog().base(2).domain([1, maxScore]).nice();
+        const [min, max] = scale.domain();
+        return { min, max };
+    }
+    const scale = scaleLinear().domain([0, maxScore]).nice();
+    const [min, max] = scale.domain();
+    return { min, max };
+}
+const HicColorLegend = observer(function HicColorLegend({ maxScore, colorScheme = 'juicebox', useLogScale, }) {
+    const { classes } = useStyles();
+    const gradient = colorGradients[colorScheme] || colorGradients.juicebox;
+    const { min, max } = getNiceScale(maxScore, useLogScale);
+    return (_jsxs("div", { className: classes.legend, children: [_jsx("div", { className: classes.gradientBar, style: { background: gradient } }), _jsxs("div", { className: classes.labels, children: [_jsx("span", { children: min !== undefined ? toLocale(min) : '' }), _jsxs("span", { children: [max !== undefined ? toLocale(max) : '', useLogScale ? ' (log)' : ''] })] })] }));
+});
+export default HicColorLegend;

package/esm/HicRenderer/components/HicRendering.d.ts

@@ -1,9 +1,2 @@
-import type { Region } from '@jbrowse/core/util/types';
-declare const HicRendering: (props: {
-    blockKey: string;
-    width: number;
-    height: number;
-    regions: Region[];
-    bpPerPx: number;
-}) => import("react/jsx-runtime").JSX.Element;
+declare const HicRendering: () => null;
 export default HicRendering;

package/esm/HicRenderer/components/HicRendering.js

@@ -1,9 +1,4 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { PrerenderedCanvas } from '@jbrowse/core/ui';
-import { observer } from 'mobx-react';
-const HicRendering = observer(function HicRendering(props) {
-    const { width, height } = props;
-    const canvasWidth = Math.ceil(width);
-    return (_jsx("div", { style: { position: 'relative', width: canvasWidth, height }, children: _jsx(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }) }));
-});
+const HicRendering = function HicRendering() {
+    return null;
+};
 export default HicRendering;

package/esm/HicRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const HicRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const HicRenderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     baseColor: {
         type: string;
         description: string;
@@ -15,5 +15,5 @@ declare const HicRenderer: import("@jbrowse/core/configuration/configurationSche
         description: string;
         defaultValue: number;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HicRenderer;

package/esm/HicRenderer/index.js

@@ -1,10 +1,10 @@
-import HicRenderer from './HicRenderer';
-import ReactComponent from './components/HicRendering';
-import configSchema from './configSchema';
+import { lazy } from 'react';
+import HicRenderer from "./HicRenderer.js";
+import configSchema from "./configSchema.js";
 export default function HicRendererF(pluginManager) {
     pluginManager.addRendererType(() => new HicRenderer({
         name: 'HicRenderer',
-        ReactComponent,
+        ReactComponent: lazy(() => import("./components/HicRendering.js")),
         configSchema,
         pluginManager,
     }));

package/esm/HicRenderer/makeImageData.d.ts

@@ -1,11 +1,18 @@
-import type { RenderArgsDeserializedWithFeatures } from './HicRenderer';
+import type { RenderArgsDeserializedWithFeatures } from './HicRenderer.tsx';
+import type { HicFlatbushItem } from './types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
 import type { Region } from '@jbrowse/core/util/types';
+export interface MakeImageDataResult {
+    flatbush: ArrayBufferLike;
+    items: HicFlatbushItem[];
+    maxScore: number;
+    w: number;
+}
 export interface RenderArgs extends ServerSideRenderArgs {
     regions: Region[];
 }
 export declare function makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures & {
     yScalar: number;
     pluginManager: PluginManager;
-}): Promise<undefined>;
+}): Promise<MakeImageDataResult | undefined>;

package/esm/HicRenderer/makeImageData.js

@@ -1,75 +1,100 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { colord } from '@jbrowse/core/util/colord';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import Flatbush from '@jbrowse/core/util/flatbush';
+import { checkStopToken2, checkStopToken, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
 import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
-import interpolateViridis from './viridis';
+import interpolateViridis from "./viridis.js";
 export async function makeImageData(ctx, props) {
     const { features, config, bpPerPx, stopToken, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, yScalar, } = props;
     const { statusCallback = () => { } } = props;
     statusCallback('Drawing Hi-C matrix');
-    const region = regions[0];
     const { dataAdapter } = await getAdapter(pluginManager, sessionId, adapterConfig);
     const res = await dataAdapter.getResolution(bpPerPx / resolution);
-    const width = (region.end - region.start) / bpPerPx;
+    const lastCheck = createStopTokenChecker(stopToken);
     const w = res / (bpPerPx * Math.sqrt(2));
     const baseColor = colord(readConfObject(config, 'baseColor'));
-    const offset = Math.floor(region.start / res);
-    if (features.length) {
-        let maxScore = 0;
-        let minBin = 0;
-        let maxBin = 0;
-        checkStopToken(stopToken);
-        for (const { bin1, bin2, counts } of features) {
-            maxScore = Math.max(counts, maxScore);
-            minBin = Math.min(Math.min(bin1, bin2), minBin);
-            maxBin = Math.max(Math.max(bin1, bin2), maxBin);
-        }
-        checkStopToken(stopToken);
-        const colorSchemes = {
-            juicebox: ['rgba(0,0,0,0)', 'red'],
-            fall: interpolateRgbBasis([
-                'rgb(255, 255, 255)',
-                'rgb(255, 255, 204)',
-                'rgb(255, 237, 160)',
-                'rgb(254, 217, 118)',
-                'rgb(254, 178, 76)',
-                'rgb(253, 141, 60)',
-                'rgb(252, 78, 42)',
-                'rgb(227, 26, 28)',
-                'rgb(189, 0, 38)',
-                'rgb(128, 0, 38)',
-                'rgb(0, 0, 0)',
-            ]),
-            viridis: interpolateViridis,
-        };
-        const m = useLogScale ? maxScore : maxScore / 20;
-        const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
-        const scale = useLogScale
-            ? scaleSequentialLog(x1).domain([1, m])
-            : scaleSequential(x1).domain([0, m]);
-        if (yScalar) {
-            ctx.scale(1, yScalar);
-        }
-        ctx.save();
-        if (region.reversed === true) {
-            ctx.scale(-1, 1);
-            ctx.translate(-width, 0);
+    const regionPixelOffsets = [];
+    let cumulativePixelOffset = 0;
+    for (const region of regions) {
+        regionPixelOffsets.push(cumulativePixelOffset);
+        cumulativePixelOffset += (region.end - region.start) / bpPerPx;
+    }
+    const regionBinOffsets = regions.map(region => Math.floor(region.start / res));
+    if (!features.length) {
+        return undefined;
+    }
+    let maxScore = 0;
+    checkStopToken(stopToken);
+    for (const { counts } of features) {
+        if (counts > maxScore) {
+            maxScore = counts;
         }
-        ctx.rotate(-Math.PI / 4);
-        forEachWithStopTokenCheck(features, stopToken, ({ bin1, bin2, counts }) => {
-            ctx.fillStyle = readConfObject(config, 'color', {
-                count: counts,
-                maxScore,
-                baseColor,
-                scale,
-                useLogScale,
-            });
-            ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
+    }
+    checkStopToken(stopToken);
+    const colorSchemes = {
+        juicebox: ['rgba(0,0,0,0)', 'red'],
+        fall: interpolateRgbBasis([
+            'rgb(255, 255, 255)',
+            'rgb(255, 255, 204)',
+            'rgb(255, 237, 160)',
+            'rgb(254, 217, 118)',
+            'rgb(254, 178, 76)',
+            'rgb(253, 141, 60)',
+            'rgb(252, 78, 42)',
+            'rgb(227, 26, 28)',
+            'rgb(189, 0, 38)',
+            'rgb(128, 0, 38)',
+            'rgb(0, 0, 0)',
+        ]),
+        viridis: interpolateViridis,
+    };
+    const m = useLogScale ? maxScore : maxScore / 20;
+    const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
+    const scale = useLogScale
+        ? scaleSequentialLog(x1).domain([1, m])
+        : scaleSequential(x1).domain([0, m]);
+    if (yScalar) {
+        ctx.scale(1, yScalar);
+    }
+    ctx.save();
+    ctx.rotate(-Math.PI / 4);
+    const pxToBinFactor = bpPerPx / res;
+    const regionCombinedOffsets = regionBinOffsets.map((binOffset, i) => (regionPixelOffsets[i] ?? 0) * pxToBinFactor - binOffset);
+    const coords = [];
+    const items = [];
+    for (let i = 0, l = features.length; i < l; i++) {
+        const { bin1, bin2, counts, region1Idx, region2Idx } = features[i];
+        ctx.fillStyle = readConfObject(config, 'color', {
+            count: counts,
+            maxScore,
+            baseColor,
+            scale,
+            useLogScale,
         });
-        ctx.restore();
+        const x = (bin1 + (regionCombinedOffsets[region1Idx] ?? 0)) * w;
+        const y = (bin2 + (regionCombinedOffsets[region2Idx] ?? 0)) * w;
+        ctx.fillRect(x, y, w, w);
+        coords.push(x, y, x + w, y + w);
+        items.push({ bin1, bin2, counts, region1Idx, region2Idx });
+        checkStopToken2(lastCheck);
+    }
+    ctx.restore();
+    const flatbush = new Flatbush(Math.max(items.length, 1));
+    if (coords.length) {
+        for (let i = 0; i < coords.length; i += 4) {
+            flatbush.add(coords[i], coords[i + 1], coords[i + 2], coords[i + 3]);
+        }
+    }
+    else {
+        flatbush.add(0, 0);
     }
-    return undefined;
+    flatbush.finish();
+    return {
+        flatbush: flatbush.data,
+        items,
+        maxScore,
+        w,
+    };
 }

package/esm/HicRenderer/types.d.ts

@@ -0,0 +1,7 @@
+export interface HicFlatbushItem {
+    bin1: number;
+    bin2: number;
+    counts: number;
+    region1Idx: number;
+    region2Idx: number;
+}

package/esm/HicRenderer/types.js

@@ -0,0 +1 @@
+export {};

package/esm/HicTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: (pluginManager: PluginManager) => import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,6 +80,6 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/esm/HicTrack/index.js

@@ -1,6 +1,6 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
-import configSchemaF from './configSchema';
+import configSchemaF from "./configSchema.js";
 export default function HicTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = configSchemaF(pluginManager);

package/esm/LinearHicDisplay/afterAttach.d.ts

@@ -0,0 +1,2 @@
+import type { LinearHicDisplayModel } from './model.ts';
+export declare function doAfterAttach(self: LinearHicDisplayModel): void;