@jbrowse/plugin-alignments 4.1.1 → 4.1.3

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -87,8 +87,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
     descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/PileupRenderer/makeImageData.js

@@ -3,7 +3,7 @@ import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { renderToAbstractCanvas } from '@jbrowse/core/util';
 import Flatbush from '@jbrowse/core/util/flatbush';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { layoutFeats } from "./layoutFeatures.js";
 import { renderAlignment } from "./renderers/renderAlignment.js";
 import { renderMismatchesCallback } from "./renderers/renderMismatchesCallback.js";
@@ -29,7 +29,7 @@ async function fetchRegionSequence(renderArgs, pluginManager) {
     });
 }
 function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
-    const { stopToken, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
+    const { stopTokenCheck, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
     const mismatchAlpha = readConfObject(config, 'mismatchAlpha');
     const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth');
     const largeInsertionIndicatorScale = readConfObject(config, 'largeInsertionIndicatorScale');
@@ -46,7 +46,6 @@ function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     const drawIndels = shouldDrawIndels();
     const coords = [];
     const items = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const feat of layoutRecords) {
         const alignmentRet = renderAlignment({
             ctx,
@@ -101,7 +100,7 @@ function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
                 canvasWidth,
             });
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const flatbush = new Flatbush(Math.max(items.length, 1));
     if (coords.length) {

package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.d.ts

@@ -1,4 +1,5 @@
 import type { ChainData, ColorBy } from '../shared/types.ts';
+import type { LastStopTokenCheck } from '@jbrowse/core/util';
 interface DrawFeatsRPCParams {
     ctx: CanvasRenderingContext2D;
     width: number;
@@ -18,7 +19,7 @@ interface DrawFeatsRPCParams {
         } | undefined;
     };
     offsetPx: number;
-    stopToken?: string;
+    stopTokenCheck?: LastStopTokenCheck;
 }
 export declare function drawFeatsRPC(params: DrawFeatsRPCParams): void;
 export {};

package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.js

@@ -1,4 +1,4 @@
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { featurizeSA, getTag } from "../MismatchParser/index.js";
 import { drawVerticalLine, extractCoreFeat, extractCoreFeatBasic, filterAndSortLongReadChain, filterPairedChain, getMateInfo, getStrandRelativeFirstClipLength, jitter, toCoreFeat, toCoreFeatBasic, } from "../shared/arcUtils.js";
 import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from "../shared/color.js";
@@ -63,7 +63,7 @@ function drawBezierArc(ctx, startX, endX, destY, jitterVal) {
     ctx.stroke();
 }
 export function drawFeatsRPC(params) {
-    const { ctx, height, chainData, colorBy, drawInter, drawLongRange, lineWidth, jitter: jitterVal, view, offsetPx, stopToken, } = params;
+    const { ctx, height, chainData, colorBy, drawInter, drawLongRange, lineWidth, jitter: jitterVal, view, offsetPx, stopTokenCheck, } = params;
     const { chains, stats } = chainData;
     const colorByType = colorBy.type;
     const hasPaired = hasPairedReads(chainData);
@@ -136,7 +136,6 @@ export function drawFeatsRPC(params) {
             draw(extractCoreFeat(filtered[i]), extractCoreFeatBasic(filtered[i + 1]), false);
         }
     }
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const chain of chains) {
         if (chain.length === 1 && drawLongRange) {
             const f = chain[0];
@@ -151,6 +150,6 @@ export function drawFeatsRPC(params) {
         else {
             drawMultiFeatureChain(chain);
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
 }

package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.js

@@ -3,7 +3,7 @@ import { collectTransferables, dedupe, groupBy, max, min, renderToAbstractCanvas
 import { bpToPx } from '@jbrowse/core/util/Base1DUtils';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { rpcResult } from '@jbrowse/core/util/librpc';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
@@ -11,6 +11,7 @@ import { drawFeatsRPC } from "./drawFeatsRPC.js";
 import { getInsertSizeStats } from "../shared/insertSizeStats.js";
 export async function executeRenderLinearReadArcsDisplay({ pluginManager, args, }) {
     const { sessionId, view: viewSnapshot, adapterConfig, sequenceAdapter, colorBy, drawInter, drawLongRange, lineWidth, jitter, height, highResolutionScaling, exportSVG, statusCallback = () => { }, stopToken, } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
     const view = Base1DView.create(viewSnapshot);
     if (viewSnapshot.width) {
         view.setVolatileWidth(viewSnapshot.width);
@@ -39,7 +40,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
         dataAdapter.setSequenceAdapterConfig(sequenceAdapter);
     }
     const featuresArray = await updateStatus('Fetching alignments', statusCallback, () => firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())));
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const { chains, stats } = await updateStatus('Processing alignments', statusCallback, async () => {
         const deduped = dedupe(featuresArray, f => f.id());
         const filtered = deduped.filter(f => {
@@ -78,7 +79,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
         chains,
         stats,
     };
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const renderOpts = {
         highResolutionScaling,
         exportSVG,
@@ -96,7 +97,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
             jitter,
             view: viewSnap,
             offsetPx,
-            stopToken,
+            stopTokenCheck,
         });
         return undefined;
     }));

package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.d.ts

@@ -3,7 +3,7 @@ import type { FlatbushItem } from '../PileupRenderer/types.ts';
 import type { FlatbushEntry } from '../shared/flatbushType.ts';
 import type { ChainData, ColorBy, ModificationTypeWithColor } from '../shared/types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
+import type { Feature, LastStopTokenCheck } from '@jbrowse/core/util';
 import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import type { ThemeOptions } from '@mui/material';
 interface ViewForDrawing {
@@ -44,7 +44,7 @@ export interface DrawFeatsParams {
     regions: BaseBlock[];
     bpPerPx: number;
     canvasWidth: number;
-    stopToken?: string;
+    stopTokenCheck?: LastStopTokenCheck;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
     hideSmallIndels?: boolean;
     hideMismatches?: boolean;

package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.js

@@ -176,7 +176,7 @@ export function addChainMouseoverRects(computedChains, chainYOffsets, featureHei
     }
 }
 export function drawFeatsCore({ ctx, params, view, calculateYOffsets, }) {
-    const { chainData, featureHeight, colorBy, drawSingletons, drawProperPairs, flipStrandLongReadChains, stopToken, } = params;
+    const { chainData, featureHeight, colorBy, drawSingletons, drawProperPairs, flipStrandLongReadChains, stopTokenCheck, } = params;
     const type = colorBy.type || 'insertSizeAndOrientation';
     const { chains } = chainData;
     const filteredChains = filterChains(chains, drawSingletons, drawProperPairs, type, chainData);
@@ -210,7 +210,7 @@ export function drawFeatsCore({ ctx, params, view, calculateYOffsets, }) {
             bpPerPx: params.bpPerPx,
             colorBy: params.colorBy,
             visibleModifications: params.visibleModifications,
-            stopToken,
+            stopTokenCheck,
             hideSmallIndels: params.hideSmallIndels,
             hideMismatches: params.hideMismatches,
             hideLargeIndels: params.hideLargeIndels,
@@ -231,7 +231,7 @@ export function drawFeatsCore({ ctx, params, view, calculateYOffsets, }) {
             bpPerPx: params.bpPerPx,
             colorBy: params.colorBy,
             visibleModifications: params.visibleModifications,
-            stopToken,
+            stopTokenCheck,
             hideSmallIndels: params.hideSmallIndels,
             hideMismatches: params.hideMismatches,
             hideLargeIndels: params.hideLargeIndels,

package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.d.ts

@@ -2,9 +2,10 @@ import type { MismatchData } from './drawChainsUtil.ts';
 import type { ComputedChain } from './drawFeatsCommon.ts';
 import type { ChainData, ColorBy, ModificationTypeWithColor } from '../shared/types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { LastStopTokenCheck } from '@jbrowse/core/util';
 import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import type { ThemeOptions } from '@mui/material';
-export declare function drawLongReadChains({ ctx, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, flipStrandLongReadChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopToken, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }: {
+export declare function drawLongReadChains({ ctx, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, flipStrandLongReadChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopTokenCheck, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }: {
     ctx: CanvasRenderingContext2D;
     chainData: ChainData;
     chainYOffsets: Map<string, number>;
@@ -19,7 +20,7 @@ export declare function drawLongReadChains({ ctx, chainData, chainYOffsets, rend
     bpPerPx: number;
     colorBy: ColorBy;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
-    stopToken?: string;
+    stopTokenCheck?: LastStopTokenCheck;
     hideSmallIndels?: boolean;
     hideMismatches?: boolean;
     hideLargeIndels?: boolean;

package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.js

@@ -1,17 +1,16 @@
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { calculateFeaturePositionPx, featureOverlapsRegion, getChainBoundsOnRef, getConnectingLineColor, getMismatchRenderingConfig, getStrandColorKey, renderFeatureMismatchesAndModifications, renderFeatureShape, } from "./drawChainsUtil.js";
 import { lineToCtx } from "../shared/canvasUtils.js";
 import { fillColor, getSingletonColor, strokeColor } from "../shared/color.js";
 import { getPrimaryStrandFromFlags } from "../shared/primaryStrand.js";
-export function drawLongReadChains({ ctx, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, flipStrandLongReadChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopToken, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }) {
+export function drawLongReadChains({ ctx, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, flipStrandLongReadChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopTokenCheck, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }) {
     const mismatchConfig = getMismatchRenderingConfig(ctx, config, configTheme, colorBy, { hideSmallIndels, hideMismatches, hideLargeIndels });
     const canvasWidth = region.widthPx;
     const regionStart = region.start;
     const allCoords = [];
     const allItems = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const computedChain of computedChains) {
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
         const { id, chain, isPairedEnd, nonSupplementary } = computedChain;
         if (isPairedEnd) {
             continue;

package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.d.ts

@@ -2,9 +2,10 @@ import type { MismatchData } from './drawChainsUtil.ts';
 import type { ComputedChain } from './drawFeatsCommon.ts';
 import type { ChainData, ColorBy, ModificationTypeWithColor } from '../shared/types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { LastStopTokenCheck } from '@jbrowse/core/util';
 import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import type { ThemeOptions } from '@mui/material';
-export declare function drawPairChains({ ctx, type, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopToken, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }: {
+export declare function drawPairChains({ ctx, type, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopTokenCheck, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }: {
     ctx: CanvasRenderingContext2D;
     type: string;
     chainData: ChainData;
@@ -19,7 +20,7 @@ export declare function drawPairChains({ ctx, type, chainData, chainYOffsets, re
     bpPerPx: number;
     colorBy: ColorBy;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
-    stopToken?: string;
+    stopTokenCheck?: LastStopTokenCheck;
     hideSmallIndels?: boolean;
     hideMismatches?: boolean;
     hideLargeIndels?: boolean;

package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.js

@@ -1,16 +1,15 @@
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { calculateFeaturePositionPx, featureOverlapsRegion, getChainBoundsOnRef, getConnectingLineColor, getMismatchRenderingConfig, renderFeatureMismatchesAndModifications, renderFeatureShape, } from "./drawChainsUtil.js";
 import { lineToCtx } from "../shared/canvasUtils.js";
 import { fillColor, getPairedColor, strokeColor } from "../shared/color.js";
-export function drawPairChains({ ctx, type, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopToken, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }) {
+export function drawPairChains({ ctx, type, chainData, chainYOffsets, renderChevrons, featureHeight, computedChains, config, theme: configTheme, region, regionStartPx, bpPerPx, colorBy, visibleModifications, stopTokenCheck, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, }) {
     const mismatchConfig = getMismatchRenderingConfig(ctx, config, configTheme, colorBy, { hideSmallIndels, hideMismatches, hideLargeIndels });
     const canvasWidth = region.widthPx;
     const regionStart = region.start;
     const allCoords = [];
     const allItems = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const computedChain of computedChains) {
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
         const { id, chain, isPairedEnd, nonSupplementary } = computedChain;
         if (!isPairedEnd) {
             continue;
@@ -89,7 +88,7 @@ export function drawPairChains({ ctx, type, chainData, chainYOffsets, renderChev
                 allItems,
             });
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return { coords: allCoords, items: allItems };
 }

package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.js

@@ -3,7 +3,7 @@ import { collectTransferables, dedupe, groupBy, max, min, renderToAbstractCanvas
 import { bpToPx } from '@jbrowse/core/util/Base1DUtils';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { rpcResult } from '@jbrowse/core/util/librpc';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
@@ -13,6 +13,7 @@ import { calculateStackYOffsetsUtil } from "./drawFeatsStack.js";
 import { getInsertSizeStats } from "../shared/insertSizeStats.js";
 export async function executeRenderLinearReadCloudDisplay({ pluginManager, args, }) {
     const { sessionId, view: viewSnapshot, adapterConfig, sequenceAdapter, config, theme, featureHeight, noSpacing, drawCloud, colorBy, drawSingletons, drawProperPairs, flipStrandLongReadChains, trackMaxHeight, cloudModeHeight, highResolutionScaling, exportSVG, statusCallback = () => { }, stopToken, visibleModifications, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
     const view = Base1DView.create(viewSnapshot);
     if (viewSnapshot.width) {
         view.setVolatileWidth(viewSnapshot.width);
@@ -45,7 +46,7 @@ export async function executeRenderLinearReadCloudDisplay({ pluginManager, args,
         dataAdapter.setSequenceAdapterConfig(sequenceAdapter);
     }
     const featuresArray = await updateStatus('Fetching alignments', statusCallback, () => firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())));
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const deduped = dedupe(featuresArray, f => f.id());
     const { chains, stats } = await updateStatus('Processing alignments', statusCallback, async () => {
         const tlens = [];
@@ -74,7 +75,7 @@ export async function executeRenderLinearReadCloudDisplay({ pluginManager, args,
         };
     });
     const chainData = { chains, stats };
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const { computedChains } = await updateStatus('Calculating layout', statusCallback, async () => {
         const filtered = filterChains(chains, drawSingletons, drawProperPairs, colorBy.type || 'insertSizeAndOrientation', chainData);
         const computed = computeChainBounds(filtered, viewSnap);
@@ -115,7 +116,7 @@ export async function executeRenderLinearReadCloudDisplay({ pluginManager, args,
                 theme,
                 regions,
                 bpPerPx,
-                stopToken,
+                stopTokenCheck,
                 visibleModifications,
                 hideSmallIndels,
                 hideMismatches,

package/esm/SNPCoverageRenderer/buildClickMap.d.ts

@@ -0,0 +1,5 @@
+import type { ClickMapItem } from './types.ts';
+export declare function buildClickMap(coords: number[], items: ClickMapItem[]): {
+    flatbush: ArrayBufferLike;
+    items: ClickMapItem[];
+};

package/esm/SNPCoverageRenderer/buildClickMap.js

@@ -0,0 +1,17 @@
+import Flatbush from '@jbrowse/core/util/flatbush';
+export 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,
+    };
+}

package/esm/SNPCoverageRenderer/calculateModificationCounts.d.ts

@@ -1,20 +1,2 @@
-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;
-}
-interface ModificationCountsResult {
-    readonly modifiable: number;
-    readonly detectable: number;
-}
+import type { ModificationCountsParams, ModificationCountsResult } from './types.ts';
 export declare function calculateModificationCounts({ base, isSimplex, refbase, snps, ref, score0, }: ModificationCountsParams): ModificationCountsResult;
-export {};

package/esm/SNPCoverageRenderer/calculateModificationCounts.js

@@ -1,9 +1,4 @@
-const complementBase = {
-    C: 'G',
-    G: 'C',
-    A: 'T',
-    T: 'A',
-};
+import { complementBase } from "./constants.js";
 export function calculateModificationCounts({ base, isSimplex, refbase, snps, ref, score0, }) {
     if (base === 'N') {
         return { modifiable: score0, detectable: score0 };

package/esm/SNPCoverageRenderer/constants.d.ts

@@ -0,0 +1,12 @@
+export declare const INTERBASE_INDICATOR_WIDTH = 7;
+export declare const INTERBASE_INDICATOR_HEIGHT = 4.5;
+export declare const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
+export declare const INTERBASE_DRAW_THRESHOLD = 0.1;
+export declare const complementBase: {
+    readonly C: "G";
+    readonly G: "C";
+    readonly A: "T";
+    readonly T: "A";
+};
+export declare const fudgeFactor = 0.6;
+export declare const SNP_CLICKMAP_THRESHOLD = 0.04;

package/esm/SNPCoverageRenderer/constants.js

@@ -0,0 +1,12 @@
+export const INTERBASE_INDICATOR_WIDTH = 7;
+export const INTERBASE_INDICATOR_HEIGHT = 4.5;
+export const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
+export const INTERBASE_DRAW_THRESHOLD = 0.1;
+export const complementBase = {
+    C: 'G',
+    G: 'C',
+    A: 'T',
+    T: 'A',
+};
+export const fudgeFactor = 0.6;
+export const SNP_CLICKMAP_THRESHOLD = 0.04;

package/esm/SNPCoverageRenderer/createInterbaseItem.d.ts

@@ -0,0 +1,7 @@
+import type { InterbaseIndicatorItem } from './types.ts';
+export declare function createInterbaseItem(maxBase: string, count: number, total: number, start: number, maxEntry?: {
+    avgLength?: number;
+    minLength?: number;
+    maxLength?: number;
+    topSequence?: string;
+}): InterbaseIndicatorItem;

package/esm/SNPCoverageRenderer/createInterbaseItem.js

@@ -0,0 +1,13 @@
+export 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,
+    };
+}

package/esm/SNPCoverageRenderer/drawCrossHatches.d.ts

@@ -0,0 +1,3 @@
+export declare function drawCrossHatches(ctx: CanvasRenderingContext2D, ticks: {
+    values: number[];
+}, width: number, toY: (n: number) => number): void;

package/esm/SNPCoverageRenderer/drawCrossHatches.js

@@ -0,0 +1,10 @@
+export 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();
+    }
+}

package/esm/SNPCoverageRenderer/drawNoncovEvents.d.ts

@@ -0,0 +1,3 @@
+import type { SecondPassContext } from './types.ts';
+import type { BaseCoverageBin } from '../shared/types.ts';
+export declare function drawNoncovEvents(passCtx: SecondPassContext, snpinfo: BaseCoverageBin, leftPx: number, score0: number, prevTotal: number, skipDraw: boolean, fstart: number): void;

package/esm/SNPCoverageRenderer/drawNoncovEvents.js

@@ -0,0 +1,56 @@
+import { INTERBASE_DRAW_THRESHOLD, INTERBASE_INDICATOR_HEIGHT, INTERBASE_INDICATOR_WIDTH, MINIMUM_INTERBASE_INDICATOR_READ_DEPTH, } from "./constants.js";
+import { createInterbaseItem } from "./createInterbaseItem.js";
+export 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));
+            }
+        }
+    }
+}

package/esm/SNPCoverageRenderer/drawSecondPassMethylation.d.ts

@@ -0,0 +1,2 @@
+import type { SecondPassContext, SecondPassStats } from './types.ts';
+export declare function drawSecondPassMethylation(passCtx: SecondPassContext): SecondPassStats;

package/esm/SNPCoverageRenderer/drawSecondPassMethylation.js

@@ -0,0 +1,30 @@
+import { checkStopToken2, featureSpanPx } from '@jbrowse/core/util';
+import { drawNoncovEvents } from "./drawNoncovEvents.js";
+import { drawStackedBars } from "./drawStackedBars.js";
+export function drawSecondPassMethylation(passCtx) {
+    const { ctx, coverageFeatures, region, bpPerPx, colorMap, toY, toHeight, stopTokenCheck, } = passCtx;
+    let snpDrawn = 0;
+    const snpSkipped = 0;
+    let lastDrawnX = Number.NEGATIVE_INFINITY;
+    let prevTotal = 0;
+    for (let i = 0, l = coverageFeatures.length; i < l; i++) {
+        checkStopToken2(stopTokenCheck);
+        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, 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);
+        snpDrawn++;
+        lastDrawnX = drawX;
+        drawNoncovEvents(passCtx, snpinfo, leftPx, score0, prevTotal, skipDraw, feature.get('start'));
+        prevTotal = score0;
+    }
+    return { snpDrawn, snpSkipped };
+}

package/esm/SNPCoverageRenderer/drawSecondPassModifications.d.ts

@@ -0,0 +1,6 @@
+import type { SecondPassContext, SecondPassStats } from './types.ts';
+export declare function drawSecondPassModifications(passCtx: SecondPassContext, visibleModifications: Record<string, {
+    base: string;
+    type: string;
+    color?: string;
+}>, isolatedModification: string | undefined, simplexSet: Set<string>): SecondPassStats;

package/esm/SNPCoverageRenderer/drawSecondPassModifications.js

@@ -0,0 +1,85 @@
+import { checkStopToken2, featureSpanPx } from '@jbrowse/core/util';
+import { calculateModificationCounts } from "./calculateModificationCounts.js";
+import { drawNoncovEvents } from "./drawNoncovEvents.js";
+import { alphaColor } from "../shared/util.js";
+export function drawSecondPassModifications(passCtx, visibleModifications, isolatedModification, simplexSet) {
+    const { ctx, coverageFeatures, region, bpPerPx, toY, toHeight, stopTokenCheck, } = 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(stopTokenCheck);
+        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: snps || {},
+                ref: ref || { entryDepth: 0, '1': 0, '-1': 0, '0': 0 },
+                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: snps || {},
+                ref: ref || { entryDepth: 0, '1': 0, '-1': 0, '0': 0 },
+                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 };
+}

package/esm/SNPCoverageRenderer/drawSecondPassSNPs.d.ts

@@ -0,0 +1,2 @@
+import type { SecondPassContext, SecondPassStats } from './types.ts';
+export declare function drawSecondPassSNPs(passCtx: SecondPassContext): SecondPassStats;

package/esm/SNPCoverageRenderer/drawSecondPassSNPs.js

@@ -0,0 +1,64 @@
+import { checkStopToken2, featureSpanPx } from '@jbrowse/core/util';
+import { SNP_CLICKMAP_THRESHOLD } from "./constants.js";
+import { drawNoncovEvents } from "./drawNoncovEvents.js";
+export function drawSecondPassSNPs(passCtx) {
+    const { ctx, coverageFeatures, region, bpPerPx, colorMap, toY, toHeight, stopTokenCheck, 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(stopTokenCheck);
+        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 };
+}

package/esm/SNPCoverageRenderer/drawStackedBars.d.ts

@@ -0,0 +1,3 @@
+export declare function drawStackedBars(ctx: CanvasRenderingContext2D, entries: Record<string, {
+    entryDepth: number;
+}>, colorMap: Record<string, string>, x: number, bottom: number, w: number, h: number, depth: number, startCurr: number): number;

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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "4.1.1",
+  "version": "4.1.3",
   "type": "module",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
@@ -34,10 +34,10 @@
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
-    "@jbrowse/plugin-wiggle": "^4.1.1",
-    "@jbrowse/sv-core": "^4.1.1"
+    "@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"