@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/shared/drawAlleleCount.js

@@ -1,24 +1,58 @@
 import { colord } from '@jbrowse/core/util/colord';
-import { f2 } from './constants';
+import { ALT_COLOR_HUE, ALT_COLOR_SATURATION, NO_CALL_COLOR, REFERENCE_COLOR, f2, } from "./constants.js";
+export function getAlleleColor(genotype, mostFrequentAlt, colorCache, splitCache, drawRef) {
+    const cacheKey = `${genotype}:${mostFrequentAlt}`;
+    let c = colorCache[cacheKey];
+    if (c === undefined) {
+        let alt = 0;
+        let uncalled = 0;
+        let alt2 = 0;
+        let ref = 0;
+        const alleles = splitCache[genotype] ?? (splitCache[genotype] = genotype.split(/[/|]/));
+        const total = alleles.length;
+        for (let i = 0; i < total; i++) {
+            const allele = alleles[i];
+            if (allele === mostFrequentAlt) {
+                alt++;
+            }
+            else if (allele === '0') {
+                ref++;
+            }
+            else if (allele === '.') {
+                uncalled++;
+            }
+            else {
+                alt2++;
+            }
+        }
+        c = getColorAlleleCount(ref, alt, alt2, uncalled, total, drawRef);
+        colorCache[cacheKey] = c;
+    }
+    return c;
+}
 export function getColorAlleleCount(ref, alt, alt2, uncalled, total, drawReference = true) {
     if (ref === total) {
-        return drawReference ? '#ccc' : '';
+        return drawReference ? REFERENCE_COLOR : '';
     }
-    else {
-        let a1;
-        if (alt) {
-            a1 = colord(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
-        }
-        if (alt2) {
-            const l = `hsla(0,100%,20%,${alt2 / total})`;
-            a1 = a1 ? a1.mix(l) : colord(l);
-        }
-        if (uncalled) {
-            const l = `hsl(50,50%,50%,${uncalled / total})`;
-            a1 = a1 ? a1.mix(l) : colord(l);
-        }
-        return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
+    if (!(alt || alt2 || uncalled)) {
+        return '';
+    }
+    let a1;
+    if (alt) {
+        const lightness = 80 - (alt / total) * 50;
+        a1 = colord(`hsl(${ALT_COLOR_HUE},${ALT_COLOR_SATURATION}%,${lightness}%)`);
+    }
+    if (alt2) {
+        const alpha = alt2 / total;
+        const l = `hsla(0,100%,20%,${alpha})`;
+        a1 = a1 ? a1.mix(l) : colord(l);
+    }
+    if (uncalled) {
+        const alpha = uncalled / total;
+        const l = NO_CALL_COLOR.replace(')', `,${alpha})`).replace('hsl', 'hsla');
+        a1 = a1 ? a1.mix(l) : colord(l);
     }
+    return a1?.toHex() || 'black';
 }
 export function drawColorAlleleCount(c, ctx, x, y, w, h, featureType = '', featureStrand, alpha = 1) {
     ctx.fillStyle = alpha !== 1 ? colord(c).alpha(alpha).toHex() : c;

package/esm/shared/drawPhased.js

@@ -1,19 +1,18 @@
 import { set1 } from '@jbrowse/core/ui/colors';
 import { colord } from '@jbrowse/core/util/colord';
-import { f2 } from './constants';
-import { colorify } from './util';
-function getColorPhased(alleles, HP, drawReference = true) {
-    const c = +alleles[HP];
-    return c ? set1[c - 1] || 'black' : drawReference ? '#ccc' : undefined;
-}
-function getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference = true) {
-    const c = +alleles[HP];
-    return c ? colorify(+PS) || 'black' : drawReference ? '#ccc' : undefined;
+import { REFERENCE_COLOR, UNPHASED_COLOR, f2 } from "./constants.js";
+function colorify(n) {
+    return `hsl(${n % 255}, 50%, 50%)`;
 }
 export function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = true, alpha = 1) {
-    const c = PS !== undefined
-        ? getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference)
-        : getColorPhased(alleles, HP, drawReference);
+    const allele = +alleles[HP];
+    const c = allele
+        ? PS !== undefined
+            ? colorify(+PS) || UNPHASED_COLOR
+            : set1[allele - 1] || UNPHASED_COLOR
+        : drawReference
+            ? REFERENCE_COLOR
+            : undefined;
     if (c) {
         ctx.fillStyle = alpha !== 1 ? colord(c).alpha(alpha).toHex() : c;
         ctx.fillRect(x - f2, y - f2, w + f2, h + f2);

package/{dist → esm/shared}/getMultiVariantFeaturesAutorun.d.ts

@@ -1,18 +1,19 @@
-import type { SampleInfo, Source } from './shared/types';
+import type { SampleInfo, Source } from './types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
+import type { StopToken } from '@jbrowse/core/util/stopToken';
 export declare function getMultiVariantFeaturesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
     sources?: Source[];
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
-    statsReadyAndRegionNotTooLarge: boolean;
+    featureDensityStatsReadyAndRegionNotTooLarge: boolean;
     adapterProps: () => Record<string, unknown>;
     setError: (error: unknown) => void;
     setFeatures: (f: Feature[]) => void;
-    setMessage: (str: string) => void;
+    setStatusMessage: (str: string) => void;
     setHasPhased: (arg: boolean) => void;
     setSampleInfo: (arg: Record<string, SampleInfo>) => void;
-    setSimplifiedFeaturesLoading: (arg: string) => void;
+    setSimplifiedFeaturesLoading: (arg: StopToken) => void;
 }): void;

package/esm/{getMultiVariantFeaturesAutorun.js → shared/getMultiVariantFeaturesAutorun.js}

@@ -2,13 +2,14 @@ import { SimpleFeature, getContainingView, getSession, } from '@jbrowse/core/uti
 import { isAbortException } from '@jbrowse/core/util/aborting';
 import { createStopToken } from '@jbrowse/core/util/stopToken';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 export function getMultiVariantFeaturesAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
             const view = getContainingView(self);
-            if (!view.initialized || !self.statsReadyAndRegionNotTooLarge) {
+            if (!view.initialized ||
+                !self.featureDensityStatsReadyAndRegionNotTooLarge) {
                 return;
             }
             const stopToken = createStopToken();
@@ -25,6 +26,11 @@ export function getMultiVariantFeaturesAutorun(self) {
                     sessionId,
                     adapterConfig,
                     stopToken,
+                    statusCallback: (arg) => {
+                        if (isAlive(self)) {
+                            self.setStatusMessage(arg);
+                        }
+                    },
                 }));
                 if (isAlive(self)) {
                     self.setHasPhased(hasPhased);
@@ -41,5 +47,6 @@ export function getMultiVariantFeaturesAutorun(self) {
         }
     }, {
         delay: 1000,
+        name: 'MultiVariantFeatures',
     }));
 }

package/esm/{getMultiVariantSourcesAutorun.d.ts → shared/getMultiVariantSourcesAutorun.d.ts}

@@ -1,11 +1,12 @@
-import type { Source } from './shared/types';
+import type { Source } from './types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { StopToken } from '@jbrowse/core/util/stopToken';
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
     adapterProps: () => Record<string, unknown>;
-    setSourcesLoading: (aborter: string) => void;
+    setSourcesLoading: (aborter: StopToken) => void;
     setError: (error: unknown) => void;
-    setMessage: (str: string) => void;
+    setStatusMessage: (str: string) => void;
     setSources: (sources: Source[]) => void;
 }): void;

package/esm/{getMultiVariantSourcesAutorun.js → shared/getMultiVariantSourcesAutorun.js}

@@ -2,8 +2,8 @@ import { getContainingView, getSession } from '@jbrowse/core/util';
 import { isAbortException } from '@jbrowse/core/util/aborting';
 import { createStopToken } from '@jbrowse/core/util/stopToken';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 export function getMultiVariantSourcesAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
@@ -20,6 +20,11 @@ export function getMultiVariantSourcesAutorun(self) {
                 sessionId,
                 adapterConfig,
                 stopToken,
+                statusCallback: (arg) => {
+                    if (isAlive(self)) {
+                        self.setStatusMessage(arg);
+                    }
+                },
             }));
             if (isAlive(self)) {
                 self.setSources(sources);
@@ -31,5 +36,8 @@ export function getMultiVariantSourcesAutorun(self) {
                 getSession(self).notifyError(`${e}`, e);
             }
         }
-    }, { delay: 1000 }));
+    }, {
+        delay: 1000,
+        name: 'GetMultiVariantSources',
+    }));
 }

package/esm/shared/getSources.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from './types';
+import type { SampleInfo, Source } from './types.ts';
 export declare function getSources({ sources, layout, renderingMode, sampleInfo, }: {
     sources: Source[];
     layout?: Source[];

package/esm/shared/getSources.js

@@ -3,8 +3,8 @@ export function getSources({ sources, layout = sources, renderingMode, sampleInf
     const sourceMap = Object.fromEntries(sources.map(s => [s.name, s]));
     for (const row of layout) {
         if (renderingMode === 'phased') {
-            const info = sampleInfo === null || sampleInfo === void 0 ? void 0 : sampleInfo[row.name];
-            if (info === null || info === void 0 ? void 0 : info.isPhased) {
+            const info = sampleInfo?.[row.name];
+            if (info?.isPhased) {
                 const ploidy = info.maxPloidy;
                 for (let i = 0; i < ploidy; i++) {
                     const id = `${row.name} HP${i}`;

package/esm/shared/hooks/useMouseTracking.d.ts

@@ -0,0 +1,6 @@
+import type { MouseState } from '../components/types.ts';
+export declare function useMouseTracking(ref: React.RefObject<HTMLDivElement | null>): {
+    mouseState: MouseState | undefined;
+    handleMouseMove: (event: React.MouseEvent) => void;
+    handleMouseLeave: () => void;
+};

package/esm/shared/hooks/useMouseTracking.js

@@ -0,0 +1,34 @@
+import { useCallback, useRef, useState } from 'react';
+export function useMouseTracking(ref) {
+    const rafRef = useRef(undefined);
+    const [mouseState, setMouseState] = useState();
+    const handleMouseMove = useCallback((event) => {
+        if (rafRef.current) {
+            cancelAnimationFrame(rafRef.current);
+        }
+        const clientX = event.clientX;
+        const clientY = event.clientY;
+        rafRef.current = requestAnimationFrame(() => {
+            const rect = ref.current?.getBoundingClientRect();
+            if (rect) {
+                setMouseState({
+                    x: clientX - rect.left,
+                    y: clientY - rect.top,
+                    offsetX: rect.left,
+                    offsetY: rect.top,
+                });
+            }
+        });
+    }, [ref]);
+    const handleMouseLeave = useCallback(() => {
+        if (rafRef.current) {
+            cancelAnimationFrame(rafRef.current);
+        }
+        setMouseState(undefined);
+    }, []);
+    return {
+        mouseState,
+        handleMouseMove,
+        handleMouseLeave,
+    };
+}

package/esm/shared/makeSidebarSvg.d.ts

@@ -0,0 +1,9 @@
+import type { LegendBarModel } from './components/types.ts';
+interface Model extends LegendBarModel {
+    hierarchy: any;
+    availableHeight: number;
+    totalHeight: number;
+    treeAreaWidth: number;
+}
+export declare function makeSidebarSvg(self: Model): Promise<import("react/jsx-runtime").JSX.Element>;
+export {};

package/esm/shared/makeSidebarSvg.js

@@ -0,0 +1,9 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { getContainingView } from '@jbrowse/core/util';
+import SvgTree from "./components/SvgTree.js";
+import LegendBar from "../shared/components/MultiVariantLegendBar.js";
+export async function makeSidebarSvg(self) {
+    const { offsetPx } = getContainingView(self);
+    const { hierarchy, showTree, treeAreaWidth, availableHeight } = self;
+    return (_jsxs("g", { id: "tree-layer", "data-testid": "tree-layer", transform: `translate(${Math.max(-offsetPx, 0)})`, clipPath: "url(#sidebarClip)", children: [_jsx("clipPath", { id: "sidebarClip", children: _jsx("rect", { x: "0", y: "0", width: "100%", height: availableHeight }) }), _jsx("g", { id: "legend-layer", transform: `translate(${showTree && hierarchy ? treeAreaWidth : 0})`, children: _jsx(LegendBar, { model: self, orientation: "left", exportSVG: true }) }), showTree ? _jsx(SvgTree, { model: self }) : null] }));
+}

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,12 +1,13 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): Record<string, number>;
+import type { Feature, LastStopTokenCheck } from '@jbrowse/core/util';
+export declare function calculateAlleleCounts(genotypes: Record<string, string>, cacheSplit: Record<string, string[]>): Record<string, number>;
 export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }: {
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache, }: {
     features: Iterable<Feature>;
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
-    stopToken?: string;
+    lastCheck?: LastStopTokenCheck;
+    genotypesCache?: Map<string, Record<string, string>>;
+    splitCache?: Record<string, string[]>;
 }): {
     feature: Feature;
     mostFrequentAlt: string;

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -1,57 +1,55 @@
-import { forEachWithStopTokenCheck, sum } from '@jbrowse/core/util';
-export function findSecondLargestNumber(arr) {
-    let firstMax = 0;
-    let secondMax = 0;
-    for (const num of arr) {
-        if (num > firstMax) {
-            secondMax = firstMax;
-            firstMax = num;
-        }
-        else if (num > secondMax && num !== firstMax) {
-            secondMax = num;
-        }
-    }
-    return secondMax;
-}
-export function calculateAlleleCounts(feat) {
-    var _a;
-    const genotypes = feat.get('genotypes');
-    const alleleCounts = { 0: 0, 1: 0, '.': 0 };
-    const cacheSplit = {};
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
+export function calculateAlleleCounts(genotypes, cacheSplit) {
+    const alleleCounts = {};
     const vals = Object.values(genotypes);
-    const len = vals.length;
-    for (let i = 0; i < len; i++) {
-        const genotype = vals[i];
-        const alleles = cacheSplit[genotype] || (cacheSplit[genotype] = genotype.split(/[/|]/));
-        for (let i = 0, len = alleles.length; i < len; i++) {
-            const a = alleles[i];
-            alleleCounts[a] = ((_a = alleleCounts[a]) !== null && _a !== void 0 ? _a : 0) + 1;
+    for (const val of vals) {
+        const genotype = val;
+        const alleles = cacheSplit[genotype] ?? (cacheSplit[genotype] = genotype.split(/[/|]/));
+        for (const allele of alleles) {
+            const a = allele;
+            alleleCounts[a] = (alleleCounts[a] || 0) + 1;
         }
     }
     return alleleCounts;
 }
 export function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(Object.values(alleleCounts)) /
-        (sum(Object.values(alleleCounts)) || 1));
+    let firstMax = 0;
+    let secondMax = 0;
+    let total = 0;
+    for (const count of Object.values(alleleCounts)) {
+        total += count;
+        if (count > firstMax) {
+            secondMax = firstMax;
+            firstMax = count;
+        }
+        else if (count > secondMax && count !== firstMax) {
+            secondMax = count;
+        }
+    }
+    return secondMax / (total || 1);
 }
 function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
     for (const [alt, altCount] of Object.entries(alleleCounts)) {
-        if (alt !== '.' && alt !== '0') {
-            if (altCount > max) {
-                mostFrequentAlt = alt;
-                max = altCount;
-            }
+        if (alt !== '.' && alt !== '0' && altCount > max) {
+            mostFrequentAlt = alt;
+            max = altCount;
         }
     }
     return mostFrequentAlt;
 }
-export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }) {
+export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache = {}, }) {
     const results = [];
-    forEachWithStopTokenCheck(features, stopToken, feature => {
+    for (const feature of features) {
         if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
-            const alleleCounts = calculateAlleleCounts(feature);
+            const featureId = feature.id();
+            let genotypes = genotypesCache?.get(featureId);
+            if (!genotypes) {
+                genotypes = feature.get('genotypes');
+                genotypesCache?.set(featureId, genotypes);
+            }
+            const alleleCounts = calculateAlleleCounts(genotypes, splitCache);
             if (calculateMinorAlleleFrequency(alleleCounts) >=
                 minorAlleleFrequencyFilter) {
                 results.push({
@@ -61,6 +59,7 @@ export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorA
                 });
             }
         }
-    });
+        checkStopToken2(lastCheck);
+    }
     return results;
 }

package/esm/shared/setupMultiVariantAutoruns.d.ts

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

package/esm/shared/setupMultiVariantAutoruns.js

@@ -0,0 +1,8 @@
+import { getMultiVariantFeaturesAutorun } from "./getMultiVariantFeaturesAutorun.js";
+import { getMultiVariantSourcesAutorun } from "./getMultiVariantSourcesAutorun.js";
+import { setupTreeDrawingAutorun } from "./treeDrawingAutorun.js";
+export function setupMultiVariantAutoruns(self) {
+    getMultiVariantSourcesAutorun(self);
+    getMultiVariantFeaturesAutorun(self);
+    setupTreeDrawingAutorun(self);
+}

package/esm/shared/treeDrawingAutorun.d.ts

@@ -0,0 +1,16 @@
+import type { ClusterHierarchyNode, HoveredTreeNode } from './components/types.ts';
+import type { Source } from './types.ts';
+interface TreeDrawingModel {
+    treeCanvas?: HTMLCanvasElement;
+    mouseoverCanvas?: HTMLCanvasElement;
+    hierarchy?: ClusterHierarchyNode;
+    treeAreaWidth: number;
+    height: number;
+    scrollTop: number;
+    rowHeight: number;
+    totalHeight: number;
+    hoveredTreeNode?: HoveredTreeNode;
+    sources?: Source[];
+}
+export declare function setupTreeDrawingAutorun(self: TreeDrawingModel): void;
+export {};

package/esm/shared/treeDrawingAutorun.js

@@ -0,0 +1,71 @@
+import { getContainingView } from '@jbrowse/core/util';
+import { addDisposer } from '@jbrowse/mobx-state-tree';
+import { autorun } from 'mobx';
+export function setupTreeDrawingAutorun(self) {
+    addDisposer(self, autorun(function treeDrawAutorun() {
+        const { treeCanvas, hierarchy, treeAreaWidth, height, scrollTop, totalHeight: _totalHeight, } = self;
+        if (!treeCanvas || !hierarchy) {
+            return;
+        }
+        const ctx = treeCanvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        ctx.clearRect(0, 0, treeAreaWidth, height);
+        ctx.translate(0, -scrollTop);
+        ctx.strokeStyle = '#0008';
+        ctx.lineWidth = 1;
+        ctx.beginPath();
+        for (const link of hierarchy.links()) {
+            const { source, target } = link;
+            const sy = source.x;
+            const ty = target.x;
+            const tx = target.y;
+            const sx = source.y;
+            ctx.moveTo(sx, sy);
+            ctx.lineTo(sx, ty);
+            ctx.moveTo(sx, ty);
+            ctx.lineTo(tx, ty);
+        }
+        ctx.stroke();
+    }, {
+        name: 'TreeDraw',
+    }));
+    addDisposer(self, autorun(function treeHoverAutorun() {
+        const { mouseoverCanvas, hierarchy, rowHeight, hoveredTreeNode, height, scrollTop, sources, totalHeight, } = self;
+        if (!mouseoverCanvas) {
+            return;
+        }
+        const ctx = mouseoverCanvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        const view = getContainingView(self);
+        const viewWidth = view.width;
+        ctx.clearRect(0, 0, viewWidth, height);
+        if (hierarchy && hoveredTreeNode && sources) {
+            ctx.save();
+            ctx.translate(0, -scrollTop);
+            ctx.fillStyle = 'rgba(255,165,0,0.2)';
+            const descendantSet = new Set(hoveredTreeNode.descendantNames);
+            for (let i = 0, l = sources.length; i < l; i++) {
+                const source = sources[i];
+                if (descendantSet.has(source.name)) {
+                    const y = (i + 0.5) * rowHeight;
+                    ctx.fillRect(0, y - rowHeight / 2, viewWidth, rowHeight);
+                }
+            }
+            const { node } = hoveredTreeNode;
+            ctx.fillStyle = 'rgba(255,165,0,0.8)';
+            ctx.beginPath();
+            ctx.arc(node.y, node.x, 4, 0, 2 * Math.PI);
+            ctx.fill();
+            ctx.strokeStyle = 'rgba(255,140,0,1)';
+            ctx.lineWidth = 1;
+            ctx.stroke();
+            ctx.restore();
+        }
+    }, { name: 'TreeHover' }));
+}

package/esm/shared/types.d.ts

@@ -1,3 +1,5 @@
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
 export interface Source {
     baseUri?: string;
     name: string;
@@ -12,3 +14,16 @@ export interface SampleInfo {
     isPhased: boolean;
     maxPloidy: number;
 }
+export interface MultiVariantRenderArgsBase extends FeatureRenderArgsDeserialized {
+    sources: Source[];
+    bpPerPx: number;
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+    height: number;
+    rowHeight: number;
+    scrollTop: number;
+    features: Map<string, Feature>;
+    renderingMode: string;
+    statusCallback?: (arg: string) => void;
+    highResolutionScaling: number;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -15,44 +15,32 @@
     "directory": "plugins/variants"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/variants",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@flatten-js/interval-tree": "^2.0.0",
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@gmod/tabix": "^3.0.1",
-    "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-circular-view": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@jbrowse/sv-core": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "@mui/x-data-grid": "^8.0.0",
+    "@flatten-js/interval-tree": "^2.0.3",
+    "@gmod/hclust": "^1.0.7",
+    "@gmod/tabix": "^3.2.2",
+    "@gmod/vcf": "^6.1.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-charts-vendor": "^8.23.0",
+    "@mui/x-data-grid": "^8.23.0",
+    "copy-to-clipboard": "^3.3.3",
     "escape-html": "^1.0.3",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "fast-deep-equal": "^3.1.3",
+    "@types/file-saver-es": "^2.0.3",
+    "file-saver-es": "^2.0.5",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "rxjs": "^7.8.2",
+    "@jbrowse/plugin-circular-view": "^4.0.0",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0",
+    "@jbrowse/sv-core": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -60,8 +48,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/variants",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/ChordVariantDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function ChordVariantDisplayF(pluginManager: PluginManager): void;