@jbrowse/plugin-variants 4.1.1 → 4.1.3

package/esm/LDRenderer/LDRenderer.js

@@ -40,7 +40,7 @@ export default class LDRenderer extends ServerSideRendererType {
                 ldData,
                 regions,
                 bpPerPx,
-                stopToken: renderProps.stopToken,
+                stopTokenCheck: renderProps.stopTokenCheck,
                 yScalar,
                 useGenomicPositions,
                 signedLD,
@@ -67,7 +67,7 @@ export default class LDRenderer extends ServerSideRendererType {
         return rpcResult(serialized, collectTransferables(serialized));
     }
     async getLDData(args) {
-        const { regions, sessionId, adapterConfig, bpPerPx, ldMetric = 'r2', minorAlleleFrequencyFilter = 0.01, lengthCutoffFilter = Number.MAX_SAFE_INTEGER, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], signedLD = false, stopToken, } = args;
+        const { regions, sessionId, adapterConfig, bpPerPx, ldMetric = 'r2', minorAlleleFrequencyFilter = 0.01, lengthCutoffFilter = Number.MAX_SAFE_INTEGER, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], signedLD = false, stopTokenCheck, } = args;
         try {
             const adapterType = adapterConfig.type;
             if (adapterType === 'PlinkLDAdapter' ||
@@ -97,7 +97,7 @@ export default class LDRenderer extends ServerSideRendererType {
                     callRateFilter,
                     jexlFilters,
                     signedLD,
-                    stopToken,
+                    stopTokenCheck,
                 },
             });
         }

package/esm/LDRenderer/makeImageData.d.ts

@@ -1,6 +1,6 @@
 import type { LDFlatbushItem } from './types.ts';
 import type { LDMatrixResult } from '../VariantRPC/getLDMatrix.ts';
-import type { Region, StopToken } from '@jbrowse/core/util';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export interface MakeImageDataResult {
     flatbush: ArrayBufferLike;
     items: LDFlatbushItem[];
@@ -11,7 +11,7 @@ export interface MakeImageDataProps {
     ldData: LDMatrixResult;
     regions: Region[];
     bpPerPx: number;
-    stopToken?: StopToken;
+    stopTokenCheck?: LastStopTokenCheck;
     yScalar: number;
     colorScheme?: string;
     useGenomicPositions?: boolean;

package/esm/LDRenderer/makeImageData.js

@@ -1,5 +1,5 @@
 import Flatbush from '@jbrowse/core/util/flatbush';
-import { checkStopToken2, checkStopToken, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
 import { scaleSequential } from '@mui/x-charts-vendor/d3-scale';
 const colorSchemes = {
@@ -59,14 +59,13 @@ const colorSchemes = {
     ]),
 };
 export function makeImageData(ctx, props) {
-    const { ldData, regions, bpPerPx, stopToken, yScalar, useGenomicPositions = false, signedLD = false, } = props;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { ldData, regions, bpPerPx, stopTokenCheck, yScalar, useGenomicPositions = false, signedLD = false, } = props;
     const { snps, ldValues, metric } = ldData;
     const n = snps.length;
     if (n === 0) {
         return undefined;
     }
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const region = regions[0];
     if (!region) {
         return undefined;
@@ -135,7 +134,7 @@ export function makeImageData(ctx, props) {
                 snp2: snps[j],
             });
             ldIdx++;
-            checkStopToken2(lastCheck);
+            checkStopToken2(stopTokenCheck);
         }
     }
     ctx.restore();

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -1,13 +1,12 @@
 import { updateStatus } from '@jbrowse/core/util';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { f2 } from "../shared/constants.js";
 import { drawColorAlleleCount, getAlleleColor, } from "../shared/drawAlleleCount.js";
 import { drawPhased } from "../shared/drawPhased.js";
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 function drawPhasedMode(drawCtx, mafs) {
-    const { ctx, sources, startRow, endRow, h, w, scrollTop, splitCache, genotypesCache, stopToken, } = drawCtx;
+    const { ctx, sources, startRow, endRow, h, w, scrollTop, splitCache, genotypesCache, stopTokenCheck, } = drawCtx;
     const arr = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (let idx = 0, l = mafs.length; idx < l; idx++) {
         const { feature } = mafs[idx];
         const arr2 = [];
@@ -69,14 +68,13 @@ function drawPhasedMode(drawCtx, mafs) {
             }
         }
         arr.push(arr2);
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return arr;
 }
 function drawAlleleCountMode(drawCtx, mafs) {
-    const { ctx, sources, startRow, endRow, h, w, scrollTop, splitCache, stopToken, colorCache, genotypesCache, } = drawCtx;
+    const { ctx, sources, startRow, endRow, h, w, scrollTop, splitCache, stopTokenCheck, colorCache, genotypesCache, } = drawCtx;
     const arr = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (let idx = 0, l = mafs.length; idx < l; idx++) {
         const { feature, mostFrequentAlt } = mafs[idx];
         const arr2 = [];
@@ -123,21 +121,20 @@ function drawAlleleCountMode(drawCtx, mafs) {
             }
         }
         arr.push(arr2);
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return arr;
 }
 export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-    const { renderingMode, minorAlleleFrequencyFilter, sources, features, stopToken, lengthCutoffFilter, rowHeight, scrollTop, statusCallback = () => { }, } = renderArgs;
+    const { renderingMode, minorAlleleFrequencyFilter, sources, features, stopTokenCheck, lengthCutoffFilter, rowHeight, scrollTop, statusCallback = () => { }, } = renderArgs;
     const h = rowHeight;
     const startRow = Math.floor(scrollTop / h);
     const endRow = Math.min(sources.length, Math.ceil((scrollTop + canvasHeight) / h));
-    const lastCheck = createStopTokenChecker(stopToken);
     const genotypesCache = new Map();
     const colorCache = {};
     const splitCache = {};
     const mafs = await updateStatus('Calculating stats', statusCallback, () => getFeaturesThatPassMinorAlleleFrequencyFilter({
-        lastCheck,
+        stopTokenCheck,
         features: features.values(),
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
@@ -157,7 +154,7 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
         splitCache,
         colorCache,
         genotypesCache,
-        stopToken,
+        stopTokenCheck,
     };
     const arr = await updateStatus('Drawing variant matrix', statusCallback, () => renderingMode === 'phased'
         ? drawPhasedMode(drawCtx, mafs)

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -1,14 +1,13 @@
 import { featureSpanPx, updateStatus } 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 { f2 } from "../shared/constants.js";
 import { drawColorAlleleCount, getAlleleColor, } from "../shared/drawAlleleCount.js";
 import { drawPhased } from "../shared/drawPhased.js";
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 function drawPhasedMode(drawCtx, itemData, mafs) {
-    const { ctx, sources, region, bpPerPx, startRow, endRow, h, drawH, scrollTop, splitCache, drawRef, genotypesCache, stopToken, } = drawCtx;
+    const { ctx, sources, region, bpPerPx, startRow, endRow, h, drawH, scrollTop, splitCache, drawRef, genotypesCache, stopTokenCheck, } = drawCtx;
     const { items, coords } = itemData;
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const { feature } of mafs) {
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const featureId = feature.id();
@@ -44,13 +43,12 @@ function drawPhasedMode(drawCtx, itemData, mafs) {
                 }
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
 }
 function drawAlleleCountMode(drawCtx, itemData, mafs, colorCache) {
-    const { ctx, sources, region, bpPerPx, startRow, endRow, h, drawH, scrollTop, splitCache, drawRef, genotypesCache, stopToken, } = drawCtx;
+    const { ctx, sources, region, bpPerPx, startRow, endRow, h, drawH, scrollTop, splitCache, drawRef, genotypesCache, stopTokenCheck, } = drawCtx;
     const { items, coords } = itemData;
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const { mostFrequentAlt, feature } of mafs) {
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         const featureId = feature.id();
@@ -78,13 +76,12 @@ function drawAlleleCountMode(drawCtx, itemData, mafs, colorCache) {
                 }
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
 }
 export async function makeImageData(ctx, props) {
-    const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, height: canvasHeight, features, regions, bpPerPx, renderingMode, stopToken, lengthCutoffFilter, referenceDrawingMode, statusCallback = () => { }, } = props;
+    const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, height: canvasHeight, features, regions, bpPerPx, renderingMode, stopTokenCheck, lengthCutoffFilter, referenceDrawingMode, statusCallback = () => { }, } = props;
     const region = regions[0];
-    const lastCheck = createStopTokenChecker(stopToken);
     const coords = [];
     const items = [];
     const colorCache = {};
@@ -96,7 +93,7 @@ export async function makeImageData(ctx, props) {
     const startRow = Math.floor(scrollTop / h);
     const endRow = Math.min(sources.length, Math.ceil((scrollTop + canvasHeight) / h));
     const mafs = await updateStatus('Calculating stats', statusCallback, () => getFeaturesThatPassMinorAlleleFrequencyFilter({
-        lastCheck,
+        stopTokenCheck,
         features: features.values(),
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
@@ -116,7 +113,7 @@ export async function makeImageData(ctx, props) {
         splitCache,
         drawRef,
         genotypesCache,
-        stopToken,
+        stopTokenCheck,
     };
     const itemData = { items, coords };
     await updateStatus('Drawing variants', statusCallback, () => {

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,11 +1,14 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name = 'MultiVariantGetGenotypeMatrix';
     async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const stopTokenCheck = createStopTokenChecker(deserializedArgs.stopToken);
         return getGenotypeMatrix({
             pluginManager: this.pluginManager,
-            args: await this.deserializeArguments(args, rpcDriverClassName),
+            args: { ...deserializedArgs, stopTokenCheck },
         });
     }
 }

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -8,6 +8,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
+        const stopTokenCheck = createStopTokenChecker(stopToken);
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         const rawFeatures = await firstValueFrom(dataAdapter
             .getFeaturesInMultipleRegions(regions, deserializedArgs)
@@ -15,11 +16,10 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         const sampleInfo = {};
         const genotypesCache = new Map();
         let hasPhased = false;
-        const lastCheck = createStopTokenChecker(stopToken);
         const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
             minorAlleleFrequencyFilter,
             lengthCutoffFilter,
-            lastCheck,
+            stopTokenCheck,
             features: rawFeatures,
             genotypesCache,
         });
@@ -47,7 +47,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: existing?.isPhased || isPhased,
                 };
             }
-            checkStopToken2(lastCheck);
+            checkStopToken2(stopTokenCheck);
         }
         return {
             hasPhased,

package/esm/VariantRPC/executeClusterGenotypeMatrix.js

@@ -1,14 +1,17 @@
 import { clusterData, toNewick } from '@gmod/hclust';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 import { getPhasedGenotypeMatrix } from "./getPhasedGenotypeMatrix.js";
 export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
-    const { renderingMode, sampleInfo } = args;
+    const { renderingMode, sampleInfo, stopToken } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
+    const argsWithCheck = { ...args, stopTokenCheck };
     const matrix = renderingMode === 'phased' && sampleInfo
         ? await getPhasedGenotypeMatrix({
             pluginManager,
-            args: { ...args, sampleInfo },
+            args: { ...argsWithCheck, sampleInfo },
         })
-        : await getGenotypeMatrix({ pluginManager, args });
+        : await getGenotypeMatrix({ pluginManager, args: argsWithCheck });
     const sampleLabels = Object.keys(matrix);
     const result = await clusterData({
         data: Object.values(matrix),

package/esm/VariantRPC/getGenotypeMatrix.d.ts

@@ -1,13 +1,12 @@
 import type { Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export declare function getGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,11 +1,10 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 const SPLITTER = /[/|]/;
 export async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopTokenCheck, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const rows = Object.fromEntries(sources.map(s => [s.name, []]));
@@ -13,7 +12,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
@@ -42,7 +41,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
                         : 1;
             rows[name].push(genotypeStatus);
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return rows;
 }

package/esm/VariantRPC/getLDMatrix.d.ts

@@ -1,7 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export type LDMetric = 'r2' | 'dprime';
 export interface FilterStats {
     totalVariants: number;
@@ -32,7 +31,7 @@ export declare function getLDMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getLDMatrix.js

@@ -1,6 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 const SPLITTER = /[/|]/;
@@ -206,8 +206,7 @@ function calculateLDStats(geno1, geno2, signedLD = false) {
     return { r2: signedLD ? r : r2, dprime };
 }
 export async function getLDMatrix({ pluginManager, args, }) {
-    const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], stopToken, ldMetric = 'r2', signedLD = false, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], stopTokenCheck, ldMetric = 'r2', signedLD = false, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const sources = await dataAdapter.getSources(regions);
@@ -238,7 +237,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
     const filteredFeatures = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: rawFeatures,
     });
@@ -339,7 +338,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
         if (dataIsPhased) {
             phasedHaplotypes.push(encodePhasedHaplotypes(genotypes, samples));
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const n = snps.length;
     const ldSize = (n * (n - 1)) / 2;
@@ -352,7 +351,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
                 : calculateLDStats(encodedGenotypes[i], encodedGenotypes[j], signedLD);
             ldValues[idx++] = ldMetric === 'dprime' ? stats.dprime : stats.r2;
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const filterStats = {
         totalVariants,

package/esm/VariantRPC/getPhasedGenotypeMatrix.d.ts

@@ -1,13 +1,12 @@
 import type { SampleInfo, Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export declare function getPhasedGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getPhasedGenotypeMatrix.js

@@ -1,10 +1,9 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, sampleInfo, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopTokenCheck, sampleInfo, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const rows = {};
@@ -19,7 +18,7 @@ export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
@@ -44,7 +43,7 @@ export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
                 }
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return rows;
 }

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -3,11 +3,11 @@ import type { Feature, LastStopTokenCheck } from '@jbrowse/core/util';
 export declare function calculateAlleleCountsFast(feature: VcfFeature): Record<string, number>;
 export declare function calculateAlleleCounts(genotypes: Record<string, string>, cacheSplit: Record<string, string[]>): Record<string, number>;
 export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache, }: {
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopTokenCheck, genotypesCache, splitCache, }: {
     features: Iterable<Feature>;
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
-    lastCheck?: LastStopTokenCheck;
+    stopTokenCheck?: LastStopTokenCheck;
     genotypesCache?: Map<string, Record<string, string>>;
     splitCache?: Record<string, string[]>;
 }): {

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -275,7 +275,7 @@ function getMostFrequentAlt(alleleCounts) {
     }
     return mostFrequentAlt;
 }
-export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache = {}, }) {
+export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopTokenCheck, genotypesCache, splitCache = {}, }) {
     const results = [];
     for (const feature of features) {
         if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
@@ -301,7 +301,7 @@ export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorA
                 });
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return results;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "4.1.1",
+  "version": "4.1.3",
   "type": "module",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
@@ -38,10 +38,10 @@
     "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/sv-core": "^4.1.1",
-    "@jbrowse/plugin-circular-view": "^4.1.1"
+    "@jbrowse/plugin-linear-genome-view": "^4.1.3",
+    "@jbrowse/core": "^4.1.3",
+    "@jbrowse/plugin-circular-view": "^4.1.3",
+    "@jbrowse/sv-core": "^4.1.3"
   },
   "peerDependencies": {
     "react": ">=18.0.0"