@jbrowse/plugin-alignments 3.2.0 → 3.3.0

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -3,4 +3,4 @@ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;
+}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -18,5 +18,5 @@ function SuppAlignments(props) {
     }
     catch (e) {
     }
-    return ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Paired alignments", children: hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null }));
+    return hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Paired alignments", children: (0, jsx_runtime_1.jsx)(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature }) })) : null;
 }

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -4,8 +4,7 @@ exports.stateModelFactory = stateModelFactory;
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
-    const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
-    return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
+    return mobx_state_tree_1.types.compose((0, BaseFeatureWidget_1.stateModelFactory)(pluginManager), mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
         type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
     }));
 }

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -13,36 +13,7 @@ export default class PileupRenderer extends BoxRendererType {
         reversed?: boolean | undefined;
         assemblyName: string;
     };
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        canvasRecordedData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    }>;
+    render(renderProps: RenderArgsDeserialized): Promise<any>;
     createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
 export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/dist/PileupRenderer/makeImageData.js

@@ -3,11 +3,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeImageData = makeImageData;
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const util_1 = require("@jbrowse/core/util");
 const renderAlignment_1 = require("./renderAlignment");
 const renderMismatches_1 = require("./renderMismatches");
 const renderSoftClipping_1 = require("./renderSoftClipping");
-const util_1 = require("./util");
+const util_2 = require("./util");
 function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     const { stopToken, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
     const mismatchAlpha = (0, configuration_1.readConfObject)(config, 'mismatchAlpha');
@@ -16,18 +16,13 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     const hideSmallIndels = (0, configuration_1.readConfObject)(config, 'hideSmallIndels');
     const defaultColor = (0, configuration_1.readConfObject)(config, 'color') === '#f0f';
     const theme = (0, ui_1.createJBrowseTheme)(configTheme);
-    const colorMap = (0, util_1.getColorBaseMap)(theme);
-    const colorContrastMap = (0, util_1.getContrastBaseMap)(theme);
+    const colorMap = (0, util_2.getColorBaseMap)(theme);
+    const colorContrastMap = (0, util_2.getContrastBaseMap)(theme);
     ctx.font = 'bold 10px Courier New,monospace';
-    const { charWidth, charHeight } = (0, util_1.getCharWidthHeight)();
-    const drawSNPsMuted = (0, util_1.shouldDrawSNPsMuted)(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
-    const drawIndels = (0, util_1.shouldDrawIndels)();
-    let start = performance.now();
-    for (const feat of layoutRecords) {
-        if (performance.now() - start > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            start = performance.now();
-        }
+    const { charWidth, charHeight } = (0, util_2.getCharWidthHeight)();
+    const drawSNPsMuted = (0, util_2.shouldDrawSNPsMuted)(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
+    const drawIndels = (0, util_2.shouldDrawIndels)();
+    (0, util_1.forEachWithStopTokenCheck)(layoutRecords, stopToken, feat => {
         (0, renderAlignment_1.renderAlignment)({
             ctx,
             feat,
@@ -66,6 +61,6 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
                 canvasWidth,
             });
         }
-    }
+    });
     return undefined;
 }

package/dist/SNPCoverageRenderer/makeImage.js

@@ -4,7 +4,6 @@ exports.makeImage = makeImage;
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const util_2 = require("../shared/util");
 const INTERBASE_INDICATOR_WIDTH = 7;
@@ -18,7 +17,7 @@ const complementBase = {
 };
 const fudgeFactor = 0.6;
 async function makeImage(ctx, props) {
-    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+    var _a;
     const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
     const theme = (0, ui_1.createJBrowseTheme)(configTheme);
     const region = regions[0];
@@ -56,35 +55,25 @@ async function makeImage(ctx, props) {
         cpg_meth: 'red',
         cpg_unmeth: 'blue',
     };
-    const feats = [...features.values()];
     ctx.fillStyle = colorMap.total;
-    let start = performance.now();
-    for (const feature of feats) {
+    (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
         const w = rightPx - leftPx + fudgeFactor;
         const score = feature.get('score');
         ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-        if (performance.now() - start > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            start = performance.now();
-        }
-    }
+    });
     let prevTotal = 0;
     const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
     const drawingModifications = colorBy.type === 'modifications';
     const drawingMethylation = colorBy.type === 'methylation';
     const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    start = performance.now();
-    for (const feature of feats) {
-        const now = performance.now();
-        if (now - start > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-        }
+    (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
         const snpinfo = feature.get('snpinfo');
@@ -92,7 +81,7 @@ async function makeImage(ctx, props) {
         const score0 = feature.get('score');
         if (drawingModifications) {
             let curr = 0;
-            const refbase = (_b = snpinfo.refbase) === null || _b === void 0 ? void 0 : _b.toUpperCase();
+            const refbase = (_a = snpinfo.refbase) === null || _a === void 0 ? void 0 : _a.toUpperCase();
             const { nonmods, mods, snps, ref } = snpinfo;
             for (const m of Object.keys(nonmods).sort().reverse()) {
                 const mod = visibleModifications[m.replace('nonmod_', '')] ||
@@ -107,14 +96,14 @@ async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                        (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                    : (((_b = snps[mod.base]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) +
+                        (((_c = snps[cmp]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_e = snps[mod.base]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                        (((_f = snps[cmp]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                    : (((_d = snps[mod.base]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                        (((_e = snps[cmp]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
@@ -139,14 +128,14 @@ async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                        (((_h = snps[cmp]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                    : (((_f = snps[mod.base]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                        (((_g = snps[cmp]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_j = snps[mod.base]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                        (((_k = snps[cmp]) === null || _k === void 0 ? void 0 : _k.entryDepth) || 0) +
+                    : (((_h = snps[mod.base]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                        (((_j = snps[cmp]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = mods[m];
@@ -228,17 +217,17 @@ async function makeImage(ctx, props) {
             }
         }
         prevTotal = score0;
-    }
+    });
     if (showArcs) {
-        for (const f of feats) {
-            if (f.get('type') !== 'skip') {
-                continue;
+        (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
+            if (feature.get('type') !== 'skip') {
+                return;
             }
-            const s = f.get('start');
-            const e = f.get('end');
+            const s = feature.get('start');
+            const e = feature.get('end');
             const [left, right] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
             ctx.beginPath();
-            const effectiveStrand = f.get('effectiveStrand');
+            const effectiveStrand = feature.get('effectiveStrand');
             const pos = 'rgba(255,200,200,0.7)';
             const neg = 'rgba(200,200,255,0.7)';
             const neutral = 'rgba(200,200,200,0.7)';
@@ -251,11 +240,11 @@ async function makeImage(ctx, props) {
             else {
                 ctx.strokeStyle = neutral;
             }
-            ctx.lineWidth = Math.log(f.get('score') + 1);
+            ctx.lineWidth = Math.log(feature.get('score') + 1);
             ctx.moveTo(left, height - offset * 2);
             ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
             ctx.stroke();
-        }
+        });
     }
     if (displayCrossHatches) {
         ctx.lineWidth = 1;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -3,4 +3,4 @@ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -12,5 +12,5 @@ export default function SuppAlignments(props) {
     }
     catch (e) {
     }
-    return (_jsx(BaseCard, { ...props, title: "Paired alignments", children: hasBreakendSplitView ? (_jsx(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature })) : null }));
+    return hasBreakendSplitView ? (_jsx(BaseCard, { ...props, title: "Paired alignments", children: _jsx(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature }) })) : null;
 }

package/esm/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,8 +1,7 @@
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
 import { types } from 'mobx-state-tree';
 export function stateModelFactory(pluginManager) {
-    const baseModel = baseModelFactory(pluginManager);
-    return types.compose(baseModel, types.model('AlignmentsFeatureWidget', {
+    return types.compose(baseModelFactory(pluginManager), types.model('AlignmentsFeatureWidget', {
         type: types.literal('AlignmentsFeatureWidget'),
     }));
 }

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -13,36 +13,7 @@ export default class PileupRenderer extends BoxRendererType {
         reversed?: boolean | undefined;
         assemblyName: string;
     };
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        canvasRecordedData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    }>;
+    render(renderProps: RenderArgsDeserialized): Promise<any>;
     createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
 export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/esm/PileupRenderer/makeImageData.js

@@ -1,6 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { renderAlignment } from './renderAlignment';
 import { renderMismatches } from './renderMismatches';
 import { renderSoftClipping } from './renderSoftClipping';
@@ -19,12 +19,7 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
     const { charWidth, charHeight } = getCharWidthHeight();
     const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
     const drawIndels = shouldDrawIndels();
-    let start = performance.now();
-    for (const feat of layoutRecords) {
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
+    forEachWithStopTokenCheck(layoutRecords, stopToken, feat => {
         renderAlignment({
             ctx,
             feat,
@@ -63,6 +58,6 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
                 canvasWidth,
             });
         }
-    }
+    });
     return undefined;
 }

package/esm/SNPCoverageRenderer/makeImage.js

@@ -1,7 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { bpSpanPx, featureSpanPx } from '@jbrowse/core/util';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { bpSpanPx, featureSpanPx, forEachWithStopTokenCheck, } from '@jbrowse/core/util';
 import { YSCALEBAR_LABEL_OFFSET, getOrigin, getScale, } from '@jbrowse/plugin-wiggle';
 import { alphaColor } from '../shared/util';
 const INTERBASE_INDICATOR_WIDTH = 7;
@@ -15,7 +14,7 @@ const complementBase = {
 };
 const fudgeFactor = 0.6;
 export async function makeImage(ctx, props) {
-    var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+    var _a;
     const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
     const theme = createJBrowseTheme(configTheme);
     const region = regions[0];
@@ -53,35 +52,25 @@ export async function makeImage(ctx, props) {
         cpg_meth: 'red',
         cpg_unmeth: 'blue',
     };
-    const feats = [...features.values()];
     ctx.fillStyle = colorMap.total;
-    let start = performance.now();
-    for (const feature of feats) {
+    forEachWithStopTokenCheck(features.values(), stopToken, feature => {
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const w = rightPx - leftPx + fudgeFactor;
         const score = feature.get('score');
         ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-    }
+    });
     let prevTotal = 0;
     const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
     const drawingModifications = colorBy.type === 'modifications';
     const drawingMethylation = colorBy.type === 'methylation';
     const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    start = performance.now();
-    for (const feature of feats) {
-        const now = performance.now();
-        if (now - start > 400) {
-            checkStopToken(stopToken);
-        }
+    forEachWithStopTokenCheck(features.values(), stopToken, feature => {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         if (feature.get('type') === 'skip') {
-            continue;
+            return;
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const snpinfo = feature.get('snpinfo');
@@ -89,7 +78,7 @@ export async function makeImage(ctx, props) {
         const score0 = feature.get('score');
         if (drawingModifications) {
             let curr = 0;
-            const refbase = (_b = snpinfo.refbase) === null || _b === void 0 ? void 0 : _b.toUpperCase();
+            const refbase = (_a = snpinfo.refbase) === null || _a === void 0 ? void 0 : _a.toUpperCase();
             const { nonmods, mods, snps, ref } = snpinfo;
             for (const m of Object.keys(nonmods).sort().reverse()) {
                 const mod = visibleModifications[m.replace('nonmod_', '')] ||
@@ -104,14 +93,14 @@ export async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                        (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                    : (((_b = snps[mod.base]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) +
+                        (((_c = snps[cmp]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_e = snps[mod.base]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                        (((_f = snps[cmp]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                    : (((_d = snps[mod.base]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
+                        (((_e = snps[cmp]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
@@ -136,14 +125,14 @@ export async function makeImage(ctx, props) {
                 const cmp = complementBase[mod.base];
                 const detectable = mod.base === 'N'
                     ? score0
-                    : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                        (((_h = snps[cmp]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                    : (((_f = snps[mod.base]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
+                        (((_g = snps[cmp]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
                         (refbase === mod.base ? ref['1'] : 0) +
                         (refbase === cmp ? ref['-1'] : 0);
                 const modifiable = mod.base === 'N'
                     ? score0
-                    : (((_j = snps[mod.base]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                        (((_k = snps[cmp]) === null || _k === void 0 ? void 0 : _k.entryDepth) || 0) +
+                    : (((_h = snps[mod.base]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
+                        (((_j = snps[cmp]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
                         (refbase === mod.base ? ref.entryDepth : 0) +
                         (refbase === cmp ? ref.entryDepth : 0);
                 const { entryDepth, avgProbability = 0 } = mods[m];
@@ -225,17 +214,17 @@ export async function makeImage(ctx, props) {
             }
         }
         prevTotal = score0;
-    }
+    });
     if (showArcs) {
-        for (const f of feats) {
-            if (f.get('type') !== 'skip') {
-                continue;
+        forEachWithStopTokenCheck(features.values(), stopToken, feature => {
+            if (feature.get('type') !== 'skip') {
+                return;
             }
-            const s = f.get('start');
-            const e = f.get('end');
+            const s = feature.get('start');
+            const e = feature.get('end');
             const [left, right] = bpSpanPx(s, e, region, bpPerPx);
             ctx.beginPath();
-            const effectiveStrand = f.get('effectiveStrand');
+            const effectiveStrand = feature.get('effectiveStrand');
             const pos = 'rgba(255,200,200,0.7)';
             const neg = 'rgba(200,200,255,0.7)';
             const neutral = 'rgba(200,200,200,0.7)';
@@ -248,11 +237,11 @@ export async function makeImage(ctx, props) {
             else {
                 ctx.strokeStyle = neutral;
             }
-            ctx.lineWidth = Math.log(f.get('score') + 1);
+            ctx.lineWidth = Math.log(feature.get('score') + 1);
             ctx.moveTo(left, height - offset * 2);
             ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
             ctx.stroke();
-        }
+        });
     }
     if (displayCrossHatches) {
         ctx.lineWidth = 1;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.2.0",
+  "version": "3.3.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,12 +38,12 @@
   "dependencies": {
     "@gmod/bam": "^5.0.0",
     "@gmod/cram": "^4.0.1",
-    "@jbrowse/core": "^3.2.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.2.0",
-    "@jbrowse/plugin-wiggle": "^3.2.0",
-    "@jbrowse/sv-core": "^3.2.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
+    "@jbrowse/core": "^3.3.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@jbrowse/plugin-wiggle": "^3.3.0",
+    "@jbrowse/sv-core": "^3.3.0",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
     "canvas2svg": "^1.0.16",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }