@jbrowse/plugin-alignments 3.1.0 → 3.3.0

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/getSAFeatures.js

@@ -22,12 +22,12 @@ export async function getSAFeatures({ view, feature, }) {
         end: clipPos + getLengthSansClipping(cigar),
     };
     const features = [feat, ...suppAlns];
-    features.forEach((f, idx) => {
+    for (const [idx, f] of features.entries()) {
         f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
         f.syntenyId = idx;
         f.mate.syntenyId = idx;
         f.mate.uniqueId = `${f.uniqueId}_mate`;
-    });
+    }
     features.sort((a, b) => a.clipPos - b.clipPos);
     return features;
 }

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/BamAdapter/BamAdapter.js

@@ -56,14 +56,18 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         const samHeader = await bam.getHeader();
         const idToName = [];
         const nameToId = {};
-        samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-            const SN = sqLine.data.find(item => item.tag === 'SN');
-            if (SN) {
-                const refName = SN.value;
-                nameToId[refName] = refId;
-                idToName[refId] = refName;
+        if (samHeader) {
+            for (const [refId, sqLine] of samHeader
+                .filter(l => l.tag === 'SQ')
+                .entries()) {
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             }
-        });
+        }
         this.samHeader = { idToName, nameToId };
         return this.samHeader;
     }
@@ -101,9 +105,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         });
         const seqChunks = await firstValueFrom(features.pipe(toArray()));
         let sequence = '';
-        seqChunks
-            .sort((a, b) => a.get('start') - b.get('start'))
-            .forEach(chunk => {
+        for (const chunk of seqChunks.sort((a, b) => a.get('start') - b.get('start'))) {
             const chunkStart = chunk.get('start');
             const chunkEnd = chunk.get('end');
             const trimStart = Math.max(start - chunkStart, 0);
@@ -111,7 +113,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             const trimLength = trimEnd - trimStart;
             const chunkSeq = chunk.get('seq') || chunk.get('residues');
             sequence += chunkSeq.slice(trimStart, trimStart + trimLength);
-        });
+        }
         if (sequence.length !== end - start) {
             throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
         }

package/esm/CramAdapter/CramAdapter.js

@@ -95,16 +95,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         const samHeader = await cram.cram.getSamHeader();
         const idToName = [];
         const nameToId = {};
-        samHeader
+        for (const [refId, sqLine] of samHeader
             .filter(l => l.tag === 'SQ')
-            .forEach((sqLine, refId) => {
+            .entries()) {
             const SN = sqLine.data.find(item => item.tag === 'SN');
             if (SN) {
                 const refName = SN.value;
                 nameToId[refName] = refId;
                 idToName[refId] = refName;
             }
-        });
+        }
         const readGroups = samHeader
             .filter(l => l.tag === 'RG')
             .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -93,12 +93,12 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                 '#CCEEFF',
                 'lightsalmon',
             ];
-            uniqueTag.forEach(value => {
+            for (const value of uniqueTag) {
                 if (!self.colorTagMap.has(value)) {
                     const totalKeys = [...self.colorTagMap.keys()].length;
                     self.colorTagMap.set(value, colorPalette[totalKeys]);
                 }
-            });
+            }
         },
         setFeatureUnderMouse(feat) {
             self.featureUnderMouseVolatile = feat;

package/esm/LinearPileupDisplay/model.js

@@ -31,14 +31,14 @@ function stateModelFactory(configSchema) {
             self.currSortBpPerPx = n;
         },
         updateVisibleModifications(uniqueModifications) {
-            uniqueModifications.forEach(value => {
+            for (const value of uniqueModifications) {
                 if (!self.visibleModifications.has(value.type)) {
                     self.visibleModifications.set(value.type, {
                         ...value,
                         color: getColorForModification(value.type),
                     });
                 }
-            });
+            }
         },
         setModificationsReady(flag) {
             self.modificationsReady = flag;

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -4,8 +4,7 @@ import { fillRectCtx, strokeRectCtx } from './util';
 import { fillColor, strokeColor } from '../shared/color';
 export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     var _a, _b, _c, _d, _e;
-    const distances = [];
-    const minXs = [];
+    const computedChains = [];
     const { chains } = chainData;
     const { height } = self;
     const featureHeight = getConf(self, 'featureHeight');
@@ -21,20 +20,21 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
                 maxX = Math.max(maxX, re);
             }
         }
-        const distance = Math.abs(maxX - minX);
-        distances.push(distance);
-        minXs.push(minX);
+        computedChains.push({
+            distance: Math.abs(maxX - minX),
+            minX,
+            chain,
+        });
     }
+    const distances = computedChains.map(d => d.distance);
     const maxD = Math.log(max(distances));
     const minD = Math.max(Math.log(min(distances)) - 1, 0);
     const scaler = (height - 20) / (maxD - minD);
     const halfHeight = featureHeight / 2 - 0.5;
-    for (let i = 0; i < chains.length; i++) {
-        const chain = chains[i];
-        const w = distances[i];
+    for (const { minX, distance, chain } of computedChains) {
+        const w = distance;
         const top = (Math.log(w) - minD) * scaler;
-        const min = minXs[i];
-        fillRectCtx(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
+        fillRectCtx(minX - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
         const c1 = chain[0];
         let primaryStrand;
         if (!(c1.flags & 2048)) {

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/PileupRenderer/renderModifications.js

@@ -3,7 +3,7 @@ import { fillRect } from './util';
 import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 import { alphaColor } from '../shared/util';
 export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    var _a, _b, _c;
+    var _a, _b;
     const { feature, topPx, heightPx } = feat;
     const { colorBy, visibleModifications = {} } = renderArgs;
     const seq = feature.get('seq');
@@ -13,28 +13,33 @@ export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, ca
     const start = feature.get('start');
     const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
     const twoColor = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.twoColor;
-    (_c = getMaxProbModAtEachPosition(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
-        const r = start + pos;
-        const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-        const mod = visibleModifications[type];
-        if (!mod) {
-            console.warn(`${type} not known yet`);
-            return;
+    const probs = getMaxProbModAtEachPosition(feature, cigarOps);
+    if (probs) {
+        let pos = 0;
+        for (const { allProbs, prob, type } of probs) {
+            const r = start + pos;
+            const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
+            const mod = visibleModifications[type];
+            if (!mod) {
+                console.warn(`${type} not known yet`);
+                return;
+            }
+            if (isolatedModification && mod.type !== isolatedModification) {
+                return;
+            }
+            const col = mod.color || 'black';
+            const s = 1 - sum(allProbs);
+            if (twoColor && s > max(allProbs)) {
+                const c = alphaColor('blue', s);
+                const w = rightPx - leftPx + 0.5;
+                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            }
+            else {
+                const c = alphaColor(col, prob);
+                const w = rightPx - leftPx + 0.5;
+                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            }
+            pos++;
         }
-        if (isolatedModification && mod.type !== isolatedModification) {
-            return;
-        }
-        const col = mod.color || 'black';
-        const s = 1 - sum(allProbs);
-        if (twoColor && s > max(allProbs)) {
-            const c = alphaColor('blue', s);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        else {
-            const c = alphaColor(col, prob);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-    });
+    }
 }

package/esm/PileupRenderer/sortUtil.js

@@ -4,7 +4,7 @@ export const sortFeature = (features, sortedBy) => {
     const featuresInCenterLine = [];
     const featuresOutsideCenter = [];
     const { pos, type } = sortedBy;
-    featureArray.forEach(innerArray => {
+    for (const innerArray of featureArray) {
         const feature = innerArray;
         const start = feature.get('start');
         const end = feature.get('end');
@@ -14,7 +14,7 @@ export const sortFeature = (features, sortedBy) => {
         else {
             featuresOutsideCenter.push(innerArray);
         }
-    });
+    }
     const isCram = featureArray.length ? featureArray[0].get('tags') : false;
     switch (type) {
         case 'Start location': {

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -39,20 +39,24 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                 opts,
                 fetchSequence: (region) => this.fetchSequence(region),
             });
-            bins.forEach((bin, index) => {
-                const start = region.start + index;
-                observer.next(new SimpleFeature({
-                    id: `${this.id}-${start}`,
-                    data: {
-                        score: bin.depth,
-                        snpinfo: bin,
-                        start,
-                        end: start + 1,
-                        refName: region.refName,
-                    },
-                }));
-            });
-            Object.entries(skipmap).forEach(([key, skip]) => {
+            let index = 0;
+            for (const bin of bins) {
+                if (bin) {
+                    const start = region.start + index;
+                    observer.next(new SimpleFeature({
+                        id: `${this.id}-${start}`,
+                        data: {
+                            score: bin.depth,
+                            snpinfo: bin,
+                            start,
+                            end: start + 1,
+                            refName: region.refName,
+                        },
+                    }));
+                }
+                index++;
+            }
+            for (const [key, skip] of Object.entries(skipmap)) {
                 observer.next(new SimpleFeature({
                     id: key,
                     data: {
@@ -64,7 +68,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                         effectiveStrand: skip.effectiveStrand,
                     },
                 }));
-            });
+            }
             observer.complete();
         }, opts.stopToken);
     }

package/esm/SNPCoverageAdapter/processModifications.js

@@ -2,45 +2,50 @@ import { max, sum } from '@jbrowse/core/util';
 import { incWithProbabilities } from './util';
 import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 export function processModifications({ feature, colorBy, region, bins, regionSequence, }) {
-    var _a, _b, _c;
+    var _a, _b;
     const fstart = feature.get('start');
     const fstrand = feature.get('strand');
     const fend = feature.get('end');
     const twoColor = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.twoColor;
     const isolatedModification = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.isolatedModification;
-    (_c = getMaxProbModAtEachPosition(feature)) === null || _c === void 0 ? void 0 : _c.forEach(({ type, prob, allProbs }, pos) => {
-        if (isolatedModification && type !== isolatedModification) {
-            return;
-        }
-        const epos = pos + fstart - region.start;
-        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-            if (bins[epos] === undefined) {
-                bins[epos] = {
-                    depth: 0,
-                    readsCounted: 0,
-                    snps: {},
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            const s = 1 - sum(allProbs);
-            const bin = bins[epos];
-            bin.refbase = regionSequence[epos];
-            if (twoColor && s > max(allProbs)) {
-                incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
+    const probs = getMaxProbModAtEachPosition(feature);
+    if (probs) {
+        let pos = 0;
+        for (const { type, prob, allProbs } of probs) {
+            if (isolatedModification && type !== isolatedModification) {
+                return;
             }
-            else {
-                incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
+            const epos = pos + fstart - region.start;
+            if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                if (bins[epos] === undefined) {
+                    bins[epos] = {
+                        depth: 0,
+                        readsCounted: 0,
+                        snps: {},
+                        ref: {
+                            probabilities: [],
+                            entryDepth: 0,
+                            '-1': 0,
+                            0: 0,
+                            1: 0,
+                        },
+                        mods: {},
+                        nonmods: {},
+                        delskips: {},
+                        noncov: {},
+                    };
+                }
+                const s = 1 - sum(allProbs);
+                const bin = bins[epos];
+                bin.refbase = regionSequence[epos];
+                if (twoColor && s > max(allProbs)) {
+                    incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
+                }
+                else {
+                    incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
+                }
             }
+            pos++;
         }
-    });
+    }
 }

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": "3.1.0",
+  "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": "^3.1.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
-    "@jbrowse/plugin-wiggle": "^3.1.0",
-    "@jbrowse/sv-core": "^3.1.0",
-    "@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": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }