@jbrowse/plugin-alignments 4.0.4 → 4.1.3

package/esm/SNPCoverageRenderer/drawStackedBars.js

@@ -0,0 +1,10 @@
+export function drawStackedBars(ctx, entries, colorMap, x, bottom, w, h, depth, startCurr) {
+    let curr = startCurr;
+    for (const base in entries) {
+        const { entryDepth } = entries[base];
+        ctx.fillStyle = colorMap[base] || 'black';
+        ctx.fillRect(x, bottom - ((entryDepth + curr) / depth) * h, w, (entryDepth / depth) * h);
+        curr += entryDepth;
+    }
+    return curr;
+}

package/esm/SNPCoverageRenderer/makeImage.d.ts

@@ -1,2 +1,2 @@
-import type { RenderArgsDeserializedWithFeatures } from './types.ts';
+import type { RenderArgsDeserializedWithFeatures } from './types';
 export declare function renderSNPCoverageToCanvas(props: RenderArgsDeserializedWithFeatures): Promise<import("librpc-web-mod").RpcResult>;

package/esm/SNPCoverageRenderer/makeImage.js

@@ -1,310 +1,15 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { checkStopToken2, createStopTokenChecker, featureSpanPx, renderToAbstractCanvas, } from '@jbrowse/core/util';
-import Flatbush from '@jbrowse/core/util/flatbush';
+import { checkStopToken2, featureSpanPx, renderToAbstractCanvas, } from '@jbrowse/core/util';
 import { rpcResult } from '@jbrowse/core/util/librpc';
 import { collectTransferables } from '@jbrowse/core/util/offscreenCanvasPonyfill';
 import { YSCALEBAR_LABEL_OFFSET, getOrigin, getScale, } from '@jbrowse/plugin-wiggle';
-import { alphaColor } from "../shared/util.js";
-const INTERBASE_INDICATOR_WIDTH = 7;
-const INTERBASE_INDICATOR_HEIGHT = 4.5;
-const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
-const INTERBASE_DRAW_THRESHOLD = 0.1;
-const complementBase = {
-    C: 'G',
-    G: 'C',
-    A: 'T',
-    T: 'A',
-};
-const fudgeFactor = 0.6;
-const SNP_CLICKMAP_THRESHOLD = 0.04;
-function createInterbaseItem(maxBase, count, total, start, maxEntry) {
-    return {
-        type: maxBase,
-        base: maxBase,
-        count,
-        total,
-        avgLength: maxEntry?.avgLength,
-        minLength: maxEntry?.minLength,
-        maxLength: maxEntry?.maxLength,
-        topSequence: maxEntry?.topSequence,
-        start,
-    };
-}
-function drawStackedBars(ctx, entries, colorMap, x, bottom, w, h, depth, startCurr) {
-    let curr = startCurr;
-    for (const base in entries) {
-        const { entryDepth } = entries[base];
-        ctx.fillStyle = colorMap[base] || 'black';
-        ctx.fillRect(x, bottom - ((entryDepth + curr) / depth) * h, w, (entryDepth / depth) * h);
-        curr += entryDepth;
-    }
-    return curr;
-}
-function drawCrossHatches(ctx, ticks, width, toY) {
-    ctx.lineWidth = 1;
-    ctx.strokeStyle = 'rgba(140,140,140,0.8)';
-    for (const tick of ticks.values) {
-        ctx.beginPath();
-        ctx.moveTo(0, Math.round(toY(tick)));
-        ctx.lineTo(width, Math.round(toY(tick)));
-        ctx.stroke();
-    }
-}
-function calculateModificationCounts({ base, isSimplex, refbase, snps, ref, score0, }) {
-    if (base === 'N') {
-        return { modifiable: score0, detectable: score0 };
-    }
-    const cmp = complementBase[base];
-    const baseCount = (snps[base]?.entryDepth || 0) + (refbase === base ? ref.entryDepth : 0);
-    const complCount = (snps[cmp]?.entryDepth || 0) + (refbase === cmp ? ref.entryDepth : 0);
-    const modifiable = baseCount + complCount;
-    const detectable = isSimplex
-        ? (snps[base]?.['1'] || 0) +
-            (snps[cmp]?.['-1'] || 0) +
-            (refbase === base ? ref['1'] : 0) +
-            (refbase === cmp ? ref['-1'] : 0)
-        : modifiable;
-    return { modifiable, detectable };
-}
-function buildClickMap(coords, items) {
-    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);
-    }
-    flatbush.finish();
-    return {
-        flatbush: flatbush.data,
-        items,
-    };
-}
-function drawNoncovEvents(passCtx, snpinfo, leftPx, score0, prevTotal, skipDraw, fstart) {
-    const { ctx, colorMap, toHeight2, extraHorizontallyFlippedOffset, coords, items, bpPerPx, indicatorThreshold, showInterbaseCounts, showInterbaseIndicators, } = passCtx;
-    let totalCount = 0;
-    let maxDepth = 0;
-    let maxBase = '';
-    let totalHeight = 0;
-    const r = 0.6;
-    const x = leftPx - r + extraHorizontallyFlippedOffset;
-    for (const base in snpinfo.noncov) {
-        const { entryDepth } = snpinfo.noncov[base];
-        totalCount += entryDepth;
-        if (entryDepth > maxDepth) {
-            maxDepth = entryDepth;
-            maxBase = base;
-        }
-    }
-    const isSignificant = score0 > 0 && totalCount > score0 * INTERBASE_DRAW_THRESHOLD;
-    const showCounts = showInterbaseCounts && (!skipDraw || isSignificant);
-    if (showCounts) {
-        for (const base in snpinfo.noncov) {
-            const { entryDepth } = snpinfo.noncov[base];
-            const barHeight = toHeight2(entryDepth);
-            ctx.fillStyle = colorMap[base];
-            ctx.fillRect(x, INTERBASE_INDICATOR_HEIGHT + totalHeight, r * 2, barHeight);
-            totalHeight += barHeight;
-        }
-    }
-    if (totalCount > 0) {
-        const maxEntry = snpinfo.noncov[maxBase];
-        if (showCounts) {
-            if (bpPerPx < 50 || isSignificant) {
-                const clickWidth = Math.max(r * 2, 2);
-                coords.push(x, INTERBASE_INDICATOR_HEIGHT, x + clickWidth, INTERBASE_INDICATOR_HEIGHT + totalHeight);
-                items.push(createInterbaseItem(maxBase, totalCount, score0, fstart, maxEntry));
-            }
-        }
-        if (showInterbaseIndicators && (!skipDraw || isSignificant)) {
-            const indicatorComparatorScore = Math.max(score0, prevTotal);
-            if (totalCount > indicatorComparatorScore * indicatorThreshold &&
-                indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
-                ctx.fillStyle = colorMap[maxBase];
-                ctx.beginPath();
-                const l = leftPx + extraHorizontallyFlippedOffset;
-                ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);
-                ctx.lineTo(l + INTERBASE_INDICATOR_WIDTH / 2, 0);
-                ctx.lineTo(l, INTERBASE_INDICATOR_HEIGHT);
-                ctx.fill();
-                const hitboxPadding = 1;
-                coords.push(l - INTERBASE_INDICATOR_WIDTH / 2 - hitboxPadding, 0, l + INTERBASE_INDICATOR_WIDTH / 2 + hitboxPadding, INTERBASE_INDICATOR_HEIGHT + hitboxPadding);
-                items.push(createInterbaseItem(maxBase, totalCount, indicatorComparatorScore, fstart, maxEntry));
-            }
-        }
-    }
-}
-function drawSecondPassModifications(passCtx, visibleModifications, isolatedModification, simplexSet) {
-    const { ctx, coverageFeatures, region, bpPerPx, toY, toHeight, lastCheck } = passCtx;
-    let snpDrawn = 0;
-    let snpSkipped = 0;
-    let lastDrawnX = Number.NEGATIVE_INFINITY;
-    let prevTotal = 0;
-    for (let i = 0, l = coverageFeatures.length; i < l; i++) {
-        checkStopToken2(lastCheck);
-        const feature = coverageFeatures[i];
-        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        const snpinfo = feature.get('snpinfo');
-        const w = Math.max(rightPx - leftPx, 1);
-        const score0 = feature.get('score');
-        const drawX = Math.round(leftPx);
-        const skipDraw = drawX === lastDrawnX;
-        let curr = 0;
-        const refbase = snpinfo.refbase?.toUpperCase();
-        const { nonmods, mods, snps, ref } = snpinfo;
-        const h = toHeight(score0);
-        const bottom = toY(score0) + h;
-        for (const key in nonmods) {
-            const modKey = key.slice(7);
-            const mod = visibleModifications[modKey];
-            if (!mod || (isolatedModification && mod.type !== isolatedModification)) {
-                continue;
-            }
-            const { modifiable, detectable } = calculateModificationCounts({
-                base: mod.base,
-                isSimplex: simplexSet.has(mod.type),
-                refbase,
-                snps,
-                ref,
-                score0,
-            });
-            const { entryDepth, avgProbability = 0 } = nonmods[key];
-            const modFraction = (modifiable / score0) * (entryDepth / detectable);
-            const barHeight = modFraction * h;
-            if (skipDraw) {
-                snpSkipped++;
-            }
-            else {
-                ctx.fillStyle = alphaColor('blue', avgProbability);
-                ctx.fillRect(drawX, bottom - (curr + barHeight), w, barHeight);
-                snpDrawn++;
-                lastDrawnX = drawX;
-            }
-            curr += barHeight;
-        }
-        for (const key in mods) {
-            const modKey = key.slice(4);
-            const mod = visibleModifications[modKey];
-            if (!mod || (isolatedModification && mod.type !== isolatedModification)) {
-                continue;
-            }
-            const { modifiable, detectable } = calculateModificationCounts({
-                base: mod.base,
-                isSimplex: simplexSet.has(mod.type),
-                refbase,
-                snps,
-                ref,
-                score0,
-            });
-            const { entryDepth, avgProbability = 0 } = mods[key];
-            const modFraction = (modifiable / score0) * (entryDepth / detectable);
-            const barHeight = modFraction * h;
-            if (skipDraw) {
-                snpSkipped++;
-            }
-            else {
-                ctx.fillStyle = alphaColor(mod.color || 'black', avgProbability);
-                ctx.fillRect(drawX, bottom - (curr + barHeight), w, barHeight);
-                snpDrawn++;
-                lastDrawnX = drawX;
-            }
-            curr += barHeight;
-        }
-        drawNoncovEvents(passCtx, snpinfo, leftPx, score0, prevTotal, skipDraw, feature.get('start'));
-        prevTotal = score0;
-    }
-    return { snpDrawn, snpSkipped };
-}
-function drawSecondPassMethylation(passCtx) {
-    const { ctx, coverageFeatures, region, bpPerPx, colorMap, toY, toHeight, lastCheck, } = passCtx;
-    let lastDrawnX = Number.NEGATIVE_INFINITY;
-    let prevTotal = 0;
-    for (let i = 0, l = coverageFeatures.length; i < l; i++) {
-        checkStopToken2(lastCheck);
-        const feature = coverageFeatures[i];
-        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        const snpinfo = feature.get('snpinfo');
-        const w = Math.max(rightPx - leftPx, 1);
-        const score0 = feature.get('score');
-        const drawX = Math.round(leftPx);
-        const skipDraw = drawX === lastDrawnX;
-        if (!skipDraw) {
-            const { depth, nonmods, mods } = snpinfo;
-            const h = toHeight(score0);
-            const bottom = toY(score0) + h;
-            const curr = drawStackedBars(ctx, mods, colorMap, drawX, bottom, w, h, depth, 0);
-            drawStackedBars(ctx, nonmods, colorMap, drawX, bottom, w, h, depth, curr);
-            lastDrawnX = drawX;
-        }
-        drawNoncovEvents(passCtx, snpinfo, leftPx, score0, prevTotal, skipDraw, feature.get('start'));
-        prevTotal = score0;
-    }
-    return { snpDrawn: 0, snpSkipped: 0 };
-}
-function drawSecondPassSNPs(passCtx) {
-    const { ctx, coverageFeatures, region, bpPerPx, colorMap, toY, toHeight, lastCheck, coords, items, } = passCtx;
-    let snpDrawn = 0;
-    let snpSkipped = 0;
-    let lastDrawnX = Number.NEGATIVE_INFINITY;
-    let lastDrawnDepth = -1;
-    let prevTotal = 0;
-    for (let i = 0, l = coverageFeatures.length; i < l; i++) {
-        checkStopToken2(lastCheck);
-        const feature = coverageFeatures[i];
-        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        const snpinfo = feature.get('snpinfo');
-        const w = Math.max(rightPx - leftPx, 1);
-        const score0 = feature.get('score');
-        const drawX = Math.round(leftPx);
-        const skipDraw = drawX === lastDrawnX;
-        const { depth, snps, refbase } = snpinfo;
-        const refbaseUpper = refbase?.toUpperCase();
-        const h = toHeight(score0);
-        const bottom = toY(score0) + h;
-        let curr = 0;
-        for (const base in snps) {
-            const entry = snps[base];
-            const { entryDepth } = entry;
-            const y1 = bottom - ((entryDepth + curr) / depth) * h;
-            const barHeight = (entryDepth / depth) * h;
-            const isSignificant = entryDepth / score0 >= SNP_CLICKMAP_THRESHOLD;
-            const sameDepthAtSameX = skipDraw && entryDepth === lastDrawnDepth;
-            if ((skipDraw && !isSignificant) || sameDepthAtSameX) {
-                snpSkipped++;
-            }
-            else {
-                ctx.fillStyle = colorMap[base] || 'black';
-                ctx.fillRect(drawX, y1, w, barHeight);
-                snpDrawn++;
-                lastDrawnX = drawX;
-                lastDrawnDepth = entryDepth;
-            }
-            if (isSignificant) {
-                coords.push(drawX, y1, drawX + w, y1 + barHeight);
-                items.push({
-                    type: 'snp',
-                    base,
-                    count: entryDepth,
-                    total: score0,
-                    refbase: refbaseUpper,
-                    avgQual: entry.avgProbability,
-                    fwdCount: entry['1'] || 0,
-                    revCount: entry['-1'] || 0,
-                    bin: snpinfo,
-                    start: feature.get('start'),
-                    end: feature.get('end'),
-                });
-            }
-            curr += entryDepth;
-        }
-        drawNoncovEvents(passCtx, snpinfo, leftPx, score0, prevTotal, skipDraw, feature.get('start'));
-        prevTotal = score0;
-    }
-    return { snpDrawn, snpSkipped };
-}
+import { buildClickMap } from "./buildClickMap.js";
+import { fudgeFactor } from "./constants.js";
+import { drawCrossHatches } from "./drawCrossHatches.js";
+import { drawSecondPassMethylation } from "./drawSecondPassMethylation.js";
+import { drawSecondPassModifications } from "./drawSecondPassModifications.js";
+import { drawSecondPassSNPs } from "./drawSecondPassSNPs.js";
 export async function renderSNPCoverageToCanvas(props) {
     const { features, regions, bpPerPx, adapterConfig } = props;
     const region = regions[0];
@@ -345,7 +50,7 @@ export async function renderSNPCoverageToCanvas(props) {
     return rpcResult(serialized, collectTransferables(rest));
 }
 function drawSNPCoverage(ctx, props, coverageFeatures) {
-    const { regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, simplexModifications = [], scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
+    const { regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, simplexModifications = [], scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopTokenCheck, } = props;
     const theme = createJBrowseTheme(configTheme);
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
@@ -384,9 +89,8 @@ function drawSNPCoverage(ctx, props, coverageFeatures) {
     const coords = [];
     const items = [];
     ctx.fillStyle = colorMap.total;
-    const lastCheck = createStopTokenChecker(stopToken);
     for (let i = 0, l = coverageFeatures.length; i < l; i++) {
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
         const feature = coverageFeatures[i];
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const w = rightPx - leftPx + fudgeFactor;
@@ -413,7 +117,7 @@ function drawSNPCoverage(ctx, props, coverageFeatures) {
         toY,
         toHeight,
         toHeight2,
-        lastCheck,
+        stopTokenCheck,
         extraHorizontallyFlippedOffset,
         coords,
         items,

package/esm/SNPCoverageRenderer/types.d.ts

@@ -1,6 +1,6 @@
 import type { BaseCoverageBin, ColorBy, ModificationTypeWithColor } from '../shared/types.ts';
 import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Feature } from '@jbrowse/core/util';
+import type { Feature, LastStopTokenCheck } from '@jbrowse/core/util';
 import type { ScaleOpts } from '@jbrowse/plugin-wiggle';
 export interface InterbaseIndicatorItem {
     type: 'insertion' | 'softclip' | 'hardclip';
@@ -67,4 +67,65 @@ export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
 export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
     features: Map<string, Feature>;
 }
+export interface SecondPassContext {
+    ctx: CanvasRenderingContext2D;
+    coverageFeatures: Feature[];
+    region: {
+        start: number;
+        end: number;
+        refName: string;
+        reversed?: boolean;
+    };
+    bpPerPx: number;
+    colorMap: Record<string, string>;
+    toY: (n: number) => number;
+    toHeight: (n: number) => number;
+    toHeight2: (n: number) => number;
+    stopTokenCheck?: LastStopTokenCheck;
+    extraHorizontallyFlippedOffset: number;
+    coords: number[];
+    items: ClickMapItem[];
+    indicatorThreshold: number;
+    showInterbaseCounts: boolean;
+    showInterbaseIndicators: boolean;
+}
+export interface SecondPassStats {
+    snpDrawn: number;
+    snpSkipped: number;
+}
+export interface StrandCounts {
+    readonly entryDepth: number;
+    readonly '1': number;
+    readonly '-1': number;
+    readonly '0': number;
+}
+export interface ModificationCountsParams {
+    readonly base: string;
+    readonly isSimplex: boolean;
+    readonly refbase: string | undefined;
+    readonly snps: Readonly<Record<string, Partial<StrandCounts>>>;
+    readonly ref: StrandCounts;
+    readonly score0: number;
+}
+export interface ModificationCountsResult {
+    readonly modifiable: number;
+    readonly detectable: number;
+}
+export interface ReducedFeature {
+    start: number;
+    end: number;
+    score: number;
+    snpinfo: BaseCoverageBin;
+    refName: string;
+}
+export interface SkipFeatureSerialized {
+    uniqueId: string;
+    type: 'skip';
+    refName: string;
+    start: number;
+    end: number;
+    strand: number;
+    score: number;
+    effectiveStrand: number;
+}
 export {};

package/esm/shared/LinearReadDisplayBaseMixin.d.ts

@@ -5,19 +5,24 @@ export declare function LinearReadDisplayBaseMixin(): import("@jbrowse/mobx-stat
 }, {
     loading: boolean;
     lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number | undefined;
     ref: HTMLCanvasElement | null;
     renderingImageData: ImageBitmap | undefined;
     renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
     statusMessage: string | undefined;
+    canvasDrawn: boolean;
 } & {
     readonly drawn: boolean;
+    readonly fullyDrawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
     setRef(ref: HTMLCanvasElement | null): void;
     setRenderingImageData(imageData: ImageBitmap | undefined): void;
     setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
     setStatusMessage(msg?: string): void;
+    setCanvasDrawn(drawn: boolean): void;
 } & {
     beforeDestroy(): void;
 } & {

package/esm/shared/createRPCRenderingSetup.d.ts

@@ -20,6 +20,7 @@ export interface RPCRenderableModel {
     ref: HTMLCanvasElement | null;
     renderingImageData?: ImageBitmap;
     setStatusMessage?: (msg: string) => void;
+    setCanvasDrawn?: (drawn: boolean) => void;
 }
 export interface RPCRenderSetupParams<T extends RPCRenderableModel, R = Record<string, unknown>> {
     self: T;

package/esm/shared/createRPCRenderingSetup.js

@@ -33,6 +33,7 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
             const stopToken = createStopToken();
             self.setRenderingStopToken(stopToken);
             self.setLoading(true);
+            self.setCanvasDrawn?.(false);
             const viewSnapshot = {
                 displayedRegions: structuredClone(view.displayedRegions),
                 bpPerPx: view.bpPerPx,
@@ -69,6 +70,7 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
         }
         catch (error) {
             if (!isAbortException(error)) {
+                console.error(error);
                 self.setError(error);
             }
         }
@@ -80,7 +82,10 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
 }
 export function setupCanvasRenderingAutorun(self) {
     createAutorun(self, async () => {
-        drawCanvasImageData(self.ref, self.renderingImageData);
+        const success = drawCanvasImageData(self.ref, self.renderingImageData);
+        if (isAlive(self)) {
+            self.setCanvasDrawn?.(success);
+        }
     }, {
         name: 'CanvasRenderAutorun',
     });

package/esm/shared/menuItems.js

@@ -1,6 +1,6 @@
 import { lazy } from 'react';
 import { getSession } from '@jbrowse/core/util';
-import FilterListIcon from '@mui/icons-material/ClearAll';
+import ClearAllIcon from '@mui/icons-material/ClearAll';
 import PaletteIcon from '@mui/icons-material/Palette';
 import { modificationData } from "./modificationData.js";
 const FilterByTagDialog = lazy(() => import("./components/FilterByTagDialog.js"));
@@ -150,7 +150,7 @@ export function getColorSchemeMenuItem(model) {
 export function getFilterByMenuItem(model) {
     return {
         label: 'Filter by',
-        icon: FilterListIcon,
+        icon: ClearAllIcon,
         onClick: () => {
             getSession(model).queueDialog((handleClose) => [
                 FilterByTagDialog,
@@ -162,7 +162,7 @@ export function getFilterByMenuItem(model) {
 export function getEditFiltersMenuItem(model) {
     return {
         label: 'Edit filters',
-        icon: FilterListIcon,
+        icon: ClearAllIcon,
         type: 'subMenu',
         subMenu: [
             {

package/package.json

@@ -1,6 +1,7 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "4.0.4",
+  "version": "4.1.3",
+  "type": "module",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -21,11 +22,11 @@
   ],
   "dependencies": {
     "@gmod/bam": "^7.1.15",
-    "@gmod/cram": "^7.0.3",
+    "@gmod/cram": "^8.0.0",
     "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/icons-material": "^7.3.6",
-    "@mui/material": "^7.3.6",
-    "@mui/x-charts-vendor": "^8.25.0",
+    "@mui/icons-material": "^7.3.7",
+    "@mui/material": "^7.3.7",
+    "@mui/x-charts-vendor": "^8.26.0",
     "canvas2svg": "^1.0.16",
     "copy-to-clipboard": "^3.3.3",
     "fast-deep-equal": "^3.1.3",
@@ -33,10 +34,10 @@
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.0.4",
-    "@jbrowse/plugin-linear-genome-view": "^4.0.4",
-    "@jbrowse/plugin-wiggle": "^4.0.4",
-    "@jbrowse/sv-core": "^4.0.4"
+    "@jbrowse/core": "^4.1.3",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.3",
+    "@jbrowse/sv-core": "^4.1.3",
+    "@jbrowse/plugin-wiggle": "^4.1.3"
   },
   "peerDependencies": {
     "react": ">=18.0.0"