@jbrowse/plugin-variants 3.0.5 → 3.1.0

package/dist/MultiLinearVariantDisplay/components/Crosshair.js

@@ -14,7 +14,7 @@ const useStyles = (0, mui_1.makeStyles)()({
     },
     cursor: {
         pointerEvents: 'none',
-        zIndex: 1000,
+        zIndex: 800,
         position: 'absolute',
     },
     color: {

package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.js

@@ -11,7 +11,7 @@ const MultiVariantTooltip_1 = __importDefault(require("../../shared/components/M
 const useStyles = (0, mui_1.makeStyles)()({
     cursor: {
         pointerEvents: 'none',
-        zIndex: 1000,
+        zIndex: 800,
         position: 'relative',
     },
 });

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -8,6 +8,7 @@ export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderAr
     mafs: {
         feature: import("@jbrowse/core/util").Feature;
         mostFrequentAlt: string;
+        alleleCounts: Map<string, number>;
     }[];
     arr: string[][];
 }>;

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -12,6 +12,6 @@ export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFilt
         bpPerPx: number;
     }, rpcDriverClassName: string): Promise<Record<string, {
         name: string;
-        genotypes: number[];
+        genotypes: string[];
     }>>;
 }

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -19,21 +19,19 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
         const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = deserializedArgs;
         const adapter = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
         const dataAdapter = adapter.dataAdapter;
-        const region = regions[0];
-        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(region, deserializedArgs).pipe((0, rxjs_1.toArray)()));
+        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe((0, rxjs_1.toArray)()));
         const genotypeFactor = new Set();
         const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
-        for (const feat of feats) {
-            const samp = feat.get('genotypes');
-            for (const { name } of sources) {
-                const s = samp[name];
-                genotypeFactor.add(s);
+        for (const { alleleCounts } of mafs) {
+            for (const alt of alleleCounts.keys()) {
+                genotypeFactor.add(alt);
             }
         }
-        const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
         const rows = {};
         for (const { feature } of mafs) {
-            const samp = feature.get('genotypes');
+            const genotypes = feature.get('genotypes');
             for (const { name } of sources) {
                 if (!rows[name]) {
                     rows[name] = {
@@ -41,7 +39,32 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
                         genotypes: [],
                     };
                 }
-                rows[name].genotypes.push(genotypeFactorMap[samp[name]]);
+                const val = genotypes[name];
+                const alleles = val.split(/[/|]/);
+                let genotypeStatus = '0';
+                let nonRefCount = 0;
+                let uncalledCount = 0;
+                for (const l of alleles) {
+                    if (l === '.') {
+                        uncalledCount++;
+                    }
+                    else if (l !== '0') {
+                        nonRefCount++;
+                    }
+                }
+                if (uncalledCount === alleles.length) {
+                    genotypeStatus = '-1';
+                }
+                else if (nonRefCount === 0) {
+                    genotypeStatus = '0';
+                }
+                else if (nonRefCount === alleles.length) {
+                    genotypeStatus = '2';
+                }
+                else {
+                    genotypeStatus = '1';
+                }
+                rows[name].genotypes.push(genotypeStatus);
             }
         }
         return rows;

package/dist/VcfAdapter/configSchema.js

@@ -18,5 +18,18 @@ const VcfAdapter = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = VcfAdapter;

package/dist/VcfTabixAdapter/configSchema.js

@@ -6,7 +6,10 @@ function x() { }
 const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
     vcfGzLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.vcf.gz',
+            locationType: 'UriLocation',
+        },
     },
     index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
         indexType: {
@@ -30,5 +33,24 @@ const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapte
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfGzLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.tbi`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 exports.default = VcfTabixAdapter;

package/dist/shared/components/ClusterDialog.js

@@ -29,6 +29,7 @@ function ClusterDialog({ model, handleClose, }) {
     const [results, setResults] = (0, react_1.useState)();
     const [error, setError] = (0, react_1.useState)();
     const [paste, setPaste] = (0, react_1.useState)('');
+    const [useCompleteMethod, setUseCompleteMethod] = (0, react_1.useState)(false);
     (0, react_1.useEffect)(() => {
         ;
         (async () => {
@@ -50,11 +51,12 @@ function ClusterDialog({ model, handleClose, }) {
                 }));
                 const entries = Object.values(ret);
                 const keys = Object.keys(ret);
+                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
                 const text = `try(library(fastcluster), silent=TRUE)
 inputMatrix<-matrix(c(${entries.map(val => val.genotypes.join(',')).join(',\n')}
 ),nrow=${entries.length},byrow=TRUE)
 rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='single')
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
 cat(resultClusters$order,sep='\\n')`;
                 setResults(text);
             }
@@ -65,14 +67,16 @@ cat(resultClusters$order,sep='\\n')`;
                 }
             }
         })();
-    }, [model]);
+    }, [model, useCompleteMethod]);
     return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Cluster by genotype", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsxs)("div", { className: classes.mgap, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible genotype data using `hclust`." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsxs)("div", { children: ["Step 1:", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
                                             (0, file_saver_1.saveAs)(new Blob([results || ''], {
                                                 type: 'text/plain;charset=utf-8',
                                             }), 'cluster.R');
                                         }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
                                             (0, copy_to_clipboard_1.default)(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useCompleteMethod, onChange: e => {
+                                                setUseCompleteMethod(e.target.checked);
+                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
                                                 setPaste(event.target.value);
                                             }, slotProps: {
                                                 input: {

package/dist/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,11 +1,9 @@
 import type { Feature } from '@jbrowse/core/util';
 export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): {
-    alleleCounts: Map<any, any>;
-    mostFrequentAlt: any;
-};
+export declare function calculateAlleleCounts(feat: Feature): Map<any, any>;
 export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): {
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number, lengthCutoffFilter?: number): {
     feature: Feature;
     mostFrequentAlt: string;
+    alleleCounts: Map<string, number>;
 }[];

package/dist/shared/minorAlleleFrequencyUtils.js

@@ -28,6 +28,13 @@ function calculateAlleleCounts(feat) {
             alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
         }
     }
+    return alleleCounts;
+}
+function calculateMinorAlleleFrequency(alleleCounts) {
+    return (findSecondLargestNumber(alleleCounts.values()) /
+        ((0, util_1.sum)(alleleCounts.values()) || 1));
+}
+function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
     for (const [alt, altCount] of alleleCounts.entries()) {
@@ -38,22 +45,20 @@ function calculateAlleleCounts(feat) {
             }
         }
     }
-    return { alleleCounts, mostFrequentAlt };
-}
-function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(alleleCounts.values()) /
-        ((0, util_1.sum)(alleleCounts.values()) || 1));
+    return mostFrequentAlt;
 }
-function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter, lengthCutoffFilter = 10) {
     const results = [];
     for (const feature of feats) {
-        if (feature.get('end') - feature.get('start') <= 10) {
-            const { mostFrequentAlt, alleleCounts } = calculateAlleleCounts(feature);
+        if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
+            const alleleCounts = calculateAlleleCounts(feature);
             if (calculateMinorAlleleFrequency(alleleCounts) >=
                 minorAlleleFrequencyFilter) {
+                const mostFrequentAlt = getMostFrequentAlt(alleleCounts);
                 results.push({
                     feature,
                     mostFrequentAlt,
+                    alleleCounts,
                 });
             }
         }

package/esm/MultiLinearVariantDisplay/components/Crosshair.js

@@ -9,7 +9,7 @@ const useStyles = makeStyles()({
     },
     cursor: {
         pointerEvents: 'none',
-        zIndex: 1000,
+        zIndex: 800,
         position: 'absolute',
     },
     color: {

package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.js

@@ -6,7 +6,7 @@ import MultiVariantTooltip from '../../shared/components/MultiVariantTooltip';
 const useStyles = makeStyles()({
     cursor: {
         pointerEvents: 'none',
-        zIndex: 1000,
+        zIndex: 800,
         position: 'relative',
     },
 });

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -8,6 +8,7 @@ export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderAr
     mafs: {
         feature: import("@jbrowse/core/util").Feature;
         mostFrequentAlt: string;
+        alleleCounts: Map<string, number>;
     }[];
     arr: string[][];
 }>;

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -12,6 +12,6 @@ export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFilt
         bpPerPx: number;
     }, rpcDriverClassName: string): Promise<Record<string, {
         name: string;
-        genotypes: number[];
+        genotypes: string[];
     }>>;
 }

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -13,21 +13,19 @@ export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRe
         const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = deserializedArgs;
         const adapter = await getAdapter(pm, sessionId, adapterConfig);
         const dataAdapter = adapter.dataAdapter;
-        const region = regions[0];
-        const feats = await firstValueFrom(dataAdapter.getFeatures(region, deserializedArgs).pipe(toArray()));
+        const feats = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe(toArray()));
         const genotypeFactor = new Set();
         const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
-        for (const feat of feats) {
-            const samp = feat.get('genotypes');
-            for (const { name } of sources) {
-                const s = samp[name];
-                genotypeFactor.add(s);
+        for (const { alleleCounts } of mafs) {
+            for (const alt of alleleCounts.keys()) {
+                genotypeFactor.add(alt);
             }
         }
-        const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
         const rows = {};
         for (const { feature } of mafs) {
-            const samp = feature.get('genotypes');
+            const genotypes = feature.get('genotypes');
             for (const { name } of sources) {
                 if (!rows[name]) {
                     rows[name] = {
@@ -35,7 +33,32 @@ export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRe
                         genotypes: [],
                     };
                 }
-                rows[name].genotypes.push(genotypeFactorMap[samp[name]]);
+                const val = genotypes[name];
+                const alleles = val.split(/[/|]/);
+                let genotypeStatus = '0';
+                let nonRefCount = 0;
+                let uncalledCount = 0;
+                for (const l of alleles) {
+                    if (l === '.') {
+                        uncalledCount++;
+                    }
+                    else if (l !== '0') {
+                        nonRefCount++;
+                    }
+                }
+                if (uncalledCount === alleles.length) {
+                    genotypeStatus = '-1';
+                }
+                else if (nonRefCount === 0) {
+                    genotypeStatus = '0';
+                }
+                else if (nonRefCount === alleles.length) {
+                    genotypeStatus = '2';
+                }
+                else {
+                    genotypeStatus = '1';
+                }
+                rows[name].genotypes.push(genotypeStatus);
             }
         }
         return rows;

package/esm/VcfAdapter/configSchema.js

@@ -16,5 +16,18 @@ const VcfAdapter = ConfigurationSchema('VcfAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default VcfAdapter;

package/esm/VcfTabixAdapter/configSchema.js

@@ -4,7 +4,10 @@ function x() { }
 const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
     vcfGzLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.vcf.gz',
+            locationType: 'UriLocation',
+        },
     },
     index: ConfigurationSchema('VcfIndex', {
         indexType: {
@@ -28,5 +31,24 @@ const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfGzLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.tbi`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 export default VcfTabixAdapter;

package/esm/shared/components/ClusterDialog.js

@@ -3,7 +3,7 @@ import { useEffect, useState } from 'react';
 import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getContainingView, getSession, isAbortException, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
 import copy from 'copy-to-clipboard';
 import { saveAs } from 'file-saver';
 import { isAlive } from 'mobx-state-tree';
@@ -23,6 +23,7 @@ export default function ClusterDialog({ model, handleClose, }) {
     const [results, setResults] = useState();
     const [error, setError] = useState();
     const [paste, setPaste] = useState('');
+    const [useCompleteMethod, setUseCompleteMethod] = useState(false);
     useEffect(() => {
         ;
         (async () => {
@@ -44,11 +45,12 @@ export default function ClusterDialog({ model, handleClose, }) {
                 }));
                 const entries = Object.values(ret);
                 const keys = Object.keys(ret);
+                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
                 const text = `try(library(fastcluster), silent=TRUE)
 inputMatrix<-matrix(c(${entries.map(val => val.genotypes.join(',')).join(',\n')}
 ),nrow=${entries.length},byrow=TRUE)
 rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='single')
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
 cat(resultClusters$order,sep='\\n')`;
                 setResults(text);
             }
@@ -59,14 +61,16 @@ cat(resultClusters$order,sep='\\n')`;
                 }
             }
         })();
-    }, [model]);
+    }, [model, useCompleteMethod]);
     return (_jsxs(Dialog, { open: true, title: "Cluster by genotype", onClose: handleClose, children: [_jsx(DialogContent, { children: _jsxs("div", { className: classes.mgap, children: [_jsx(Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible genotype data using `hclust`." }), _jsx(Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? (_jsx("div", { children: _jsxs("div", { children: ["Step 1:", ' ', _jsx(Button, { variant: "contained", onClick: () => {
                                             saveAs(new Blob([results || ''], {
                                                 type: 'text/plain;charset=utf-8',
                                             }), 'cluster.R');
                                         }, children: "Download Rscript" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
                                             copy(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), _jsx("div", { children: _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                        }, children: "Copy Rscript to clipboard" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCompleteMethod, onChange: e => {
+                                                setUseCompleteMethod(e.target.checked);
+                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), _jsx("div", { children: _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
                                                 setPaste(event.target.value);
                                             }, slotProps: {
                                                 input: {

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,11 +1,9 @@
 import type { Feature } from '@jbrowse/core/util';
 export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): {
-    alleleCounts: Map<any, any>;
-    mostFrequentAlt: any;
-};
+export declare function calculateAlleleCounts(feat: Feature): Map<any, any>;
 export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): {
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number, lengthCutoffFilter?: number): {
     feature: Feature;
     mostFrequentAlt: string;
+    alleleCounts: Map<string, number>;
 }[];

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -22,6 +22,13 @@ export function calculateAlleleCounts(feat) {
             alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
         }
     }
+    return alleleCounts;
+}
+export function calculateMinorAlleleFrequency(alleleCounts) {
+    return (findSecondLargestNumber(alleleCounts.values()) /
+        (sum(alleleCounts.values()) || 1));
+}
+function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
     for (const [alt, altCount] of alleleCounts.entries()) {
@@ -32,22 +39,20 @@ export function calculateAlleleCounts(feat) {
             }
         }
     }
-    return { alleleCounts, mostFrequentAlt };
-}
-export function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(alleleCounts.values()) /
-        (sum(alleleCounts.values()) || 1));
+    return mostFrequentAlt;
 }
-export function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+export function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter, lengthCutoffFilter = 10) {
     const results = [];
     for (const feature of feats) {
-        if (feature.get('end') - feature.get('start') <= 10) {
-            const { mostFrequentAlt, alleleCounts } = calculateAlleleCounts(feature);
+        if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
+            const alleleCounts = calculateAlleleCounts(feature);
             if (calculateMinorAlleleFrequency(alleleCounts) >=
                 minorAlleleFrequencyFilter) {
+                const mostFrequentAlt = getMostFrequentAlt(alleleCounts);
                 results.push({
                     feature,
                     mostFrequentAlt,
+                    alleleCounts,
                 });
             }
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.0.5",
+  "version": "3.1.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -40,10 +40,10 @@
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/tabix": "^2.0.0",
     "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.0.5",
-    "@jbrowse/plugin-circular-view": "^3.0.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.5",
-    "@jbrowse/sv-core": "^3.0.5",
+    "@jbrowse/core": "^3.1.0",
+    "@jbrowse/plugin-circular-view": "^3.1.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
+    "@jbrowse/sv-core": "^3.1.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
 }