@jbrowse/plugin-variants 3.1.0 → 3.2.0

package/esm/shared/MultiVariantBaseModel.js

@@ -3,15 +3,17 @@ import { ConfigurationReference } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { stopStopToken } from '@jbrowse/core/util/stopToken';
 import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view';
+import CategoryIcon from '@mui/icons-material/Category';
 import FilterListIcon from '@mui/icons-material/FilterList';
 import HeightIcon from '@mui/icons-material/Height';
 import SplitscreenIcon from '@mui/icons-material/Splitscreen';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import deepEqual from 'fast-deep-equal';
 import { types } from 'mobx-state-tree';
+import { getSources } from './getSources';
 const SetColorDialog = lazy(() => import('./components/SetColorDialog'));
 const MAFFilterDialog = lazy(() => import('./components/MAFFilterDialog'));
-const ClusterDialog = lazy(() => import('./components/ClusterDialog'));
+const ClusterDialog = lazy(() => import('./components/ClusterDialog/ClusterDialog'));
 const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'));
 export default function MultiVariantBaseModelF(configSchema) {
     return types
@@ -86,40 +88,26 @@ export default function MultiVariantBaseModelF(configSchema) {
         get preSources() {
             return self.layout.length ? self.layout : self.sourcesVolatile;
         },
+        get sourcesWithoutLayout() {
+            return self.sourcesVolatile
+                ? getSources({
+                    sources: self.sourcesVolatile,
+                    renderingMode: self.renderingMode,
+                    sampleInfo: self.sampleInfo,
+                })
+                : undefined;
+        },
         get sources() {
-            var _a, _b;
-            if (this.preSources) {
-                const rows = [];
-                const sources = Object.fromEntries(((_a = self.sourcesVolatile) === null || _a === void 0 ? void 0 : _a.map(s => [s.name, s])) || []);
-                for (const row of this.preSources) {
-                    if (self.renderingMode === 'phased') {
-                        const info = (_b = self.sampleInfo) === null || _b === void 0 ? void 0 : _b[row.name];
-                        if (info === null || info === void 0 ? void 0 : info.isPhased) {
-                            const ploidy = info.maxPloidy;
-                            for (let i = 0; i < ploidy; i++) {
-                                const id = `${row.name} HP${i}`;
-                                rows.push({
-                                    ...sources[row.name],
-                                    ...row,
-                                    label: id,
-                                    HP: i,
-                                    id: id,
-                                });
-                            }
-                        }
-                    }
-                    else {
-                        rows.push({
-                            ...sources[row.name],
-                            ...row,
-                            label: row.name,
-                            id: row.name,
-                        });
-                    }
-                }
-                return rows;
-            }
-            return undefined;
+            const sourcesWithLayout = self.layout.length
+                ? self.layout
+                : self.sourcesVolatile;
+            return sourcesWithLayout
+                ? getSources({
+                    sources: sourcesWithLayout,
+                    renderingMode: self.renderingMode,
+                    sampleInfo: self.sampleInfo,
+                })
+                : undefined;
         },
     }))
         .views(self => {
@@ -222,6 +210,7 @@ export default function MultiVariantBaseModelF(configSchema) {
                     },
                     {
                         label: 'Cluster by genotype',
+                        icon: CategoryIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 ClusterDialog,
@@ -256,13 +245,16 @@ export default function MultiVariantBaseModelF(configSchema) {
             var _a;
             return self.rowHeight * (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
         },
+        get featuresReady() {
+            return !!self.featuresVolatile;
+        },
     }))
         .views(self => ({
         renderProps() {
             const superProps = self.adapterProps();
             return {
                 ...superProps,
-                notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
+                notReady: superProps.notReady || !self.sources || !self.featuresReady,
                 height: self.height,
                 totalHeight: self.totalHeight,
                 renderingMode: self.renderingMode,

package/esm/shared/components/ClusterDialog/ClusterDialog.d.ts

@@ -0,0 +1,6 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialog: ({ model, handleClose, }: {
+    model: ReducedModel;
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialog;

package/esm/shared/components/ClusterDialog/ClusterDialog.js

@@ -0,0 +1,24 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { FormControlLabel, Radio, RadioGroup, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import ClusterDialogAuto from './ClusterDialogAuto';
+import ClusterDialogManual from './ClusterDialogManual';
+function Header({ activeMode, setActiveMode, }) {
+    return (_jsxs("div", { children: [_jsx(Typography, { style: { marginBottom: 30 }, children: "This procedure will cluster the visible genotype data using hierarchical clustering" }), _jsx(RadioGroup, { children: Object.entries({
+                    auto: (_jsx("div", { children: "Run in-app clustering (slow for large data, built in JS clustering)" })),
+                    manual: (_jsx("div", { children: "Download R script to run clustering (faster for large data, uses hclust, may be more accurate)" })),
+                }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: activeMode === key, onChange: () => {
+                            setActiveMode(key);
+                        } }), label: val }, key))) })] }));
+}
+const ClusterDialog = observer(function ({ model, handleClose, }) {
+    const [activeMode, setActiveMode] = useState('auto');
+    return (_jsx(Dialog, { open: true, title: "Cluster by genotype", onClose: (_, reason) => {
+            if (reason !== 'backdropClick') {
+                handleClose();
+            }
+        }, children: activeMode === 'auto' ? (_jsx(ClusterDialogAuto, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : (_jsx(ClusterDialogManual, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
+});
+export default ClusterDialog;

package/esm/shared/components/ClusterDialog/ClusterDialogAuto.d.ts

@@ -0,0 +1,7 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialogAuto: ({ model, children, handleClose, }: {
+    model: ReducedModel;
+    children: React.ReactNode;
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialogAuto;

package/esm/shared/components/ClusterDialog/ClusterDialogAuto.js

@@ -0,0 +1,67 @@
+import { jsxs as _jsxs, jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
+import { useState } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { getContainingView, getSession, isAbortException, } from '@jbrowse/core/util';
+import { createStopToken, stopStopToken } from '@jbrowse/core/util/stopToken';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { Button, DialogActions, DialogContent } from '@mui/material';
+import { observer } from 'mobx-react';
+import { isAlive } from 'mobx-state-tree';
+const ClusterDialogAuto = observer(function ({ model, children, handleClose, }) {
+    const [progress, setProgress] = useState('');
+    const [error, setError] = useState();
+    const [stopToken, setStopToken] = useState('');
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs("div", { children: [progress ? (_jsxs("div", { style: { padding: 50 }, children: [_jsxs("span", { style: { width: 400 }, children: ["Progress: ", progress] }), _jsx(Button, { onClick: () => {
+                                            stopStopToken(stopToken);
+                                        }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: async () => {
+                            try {
+                                setError(undefined);
+                                const view = getContainingView(model);
+                                if (!view.initialized) {
+                                    return;
+                                }
+                                const { rpcManager } = getSession(model);
+                                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, adapterConfig, } = model;
+                                if (sourcesWithoutLayout) {
+                                    const sessionId = getRpcSessionId(model);
+                                    const stopToken = createStopToken();
+                                    setStopToken(stopToken);
+                                    const ret = (await rpcManager.call(sessionId, 'MultiVariantClusterGenotypeMatrix', {
+                                        regions: view.dynamicBlocks.contentBlocks,
+                                        sources: sourcesWithoutLayout,
+                                        minorAlleleFrequencyFilter,
+                                        sessionId,
+                                        adapterConfig,
+                                        stopToken,
+                                        statusCallback: (arg) => {
+                                            setProgress(arg);
+                                        },
+                                    }));
+                                    model.setLayout(ret.order.map(idx => {
+                                        const ret = sourcesWithoutLayout[idx];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                handleClose();
+                            }
+                            catch (e) {
+                                if (!isAbortException(e) && isAlive(model)) {
+                                    console.error(e);
+                                    setError(e);
+                                }
+                            }
+                            finally {
+                                setProgress('');
+                                setStopToken('');
+                            }
+                        }, children: "Run clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                            if (stopToken) {
+                                stopStopToken(stopToken);
+                            }
+                        }, children: "Cancel" })] })] }));
+});
+export default ClusterDialogAuto;

package/esm/shared/components/ClusterDialog/ClusterDialogManual.d.ts

@@ -0,0 +1,7 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialogManuals: ({ model, handleClose, children, }: {
+    model: ReducedModel;
+    handleClose: () => void;
+    children: React.ReactNode;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialogManuals;

package/esm/shared/components/ClusterDialog/ClusterDialogManual.js

@@ -0,0 +1,139 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getContainingView, getSession, isAbortException, useLocalStorage, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { Button, DialogActions, DialogContent, FormControlLabel, Paper, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import copy from 'copy-to-clipboard';
+import { saveAs } from 'file-saver';
+import { observer } from 'mobx-react';
+import { isAlive } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    mgap: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: theme.spacing(4),
+    },
+}));
+const ClusterDialogManuals = observer(function ({ model, handleClose, children, }) {
+    const { classes } = useStyles();
+    const [paste, setPaste] = useState('');
+    const [ret, setRet] = useState();
+    const [error, setError] = useState();
+    const [loading, setLoading] = useState(false);
+    const [showAdvanced, setShowAdvanced] = useState(false);
+    const [clusterMethod, setClusterMethod] = useLocalStorage('cluster-clusterMethod', 'single');
+    useEffect(() => {
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                setRet(undefined);
+                setLoading(true);
+                const view = getContainingView(model);
+                if (!view.initialized) {
+                    return;
+                }
+                const { rpcManager } = getSession(model);
+                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, adapterConfig, } = model;
+                const sessionId = getRpcSessionId(model);
+                const ret = (await rpcManager.call(sessionId, 'MultiVariantGetGenotypeMatrix', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources: sourcesWithoutLayout,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                setRet(ret);
+            }
+            catch (e) {
+                if (!isAbortException(e) && isAlive(model)) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [model]);
+    const results = ret
+        ? `inputMatrix<-matrix(c(${Object.values(ret)
+            .map(val => val.join(','))
+            .join(',\n')}
+),nrow=${Object.values(ret).length},byrow=TRUE)
+rownames(inputMatrix)<-c(${Object.keys(ret)
+            .map(key => `'${key}'`)
+            .join(',')})
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
+cat(resultClusters$order,sep='\\n')`
+        : undefined;
+    const resultsTsv = ret
+        ? Object.entries(ret)
+            .map(([key, val]) => [key, ...val].join('\t'))
+            .join('\n')
+        : undefined;
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs(Paper, { style: { padding: 16 }, children: [_jsxs("div", { style: {
+                                    display: 'flex',
+                                    gap: '8px',
+                                    flexWrap: 'wrap',
+                                    marginBottom: '16px',
+                                }, children: [_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" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
+                                            saveAs(new Blob([resultsTsv || ''], {
+                                                type: 'text/plain;charset=utf-8',
+                                            }), 'genotypes.tsv');
+                                        }, children: "Download TSV" }), _jsxs("div", { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                                                    setShowAdvanced(!showAdvanced);
+                                                }, children: showAdvanced
+                                                    ? 'Hide advanced options'
+                                                    : 'Show advanced options' }), showAdvanced ? (_jsxs("div", { children: [_jsx(Typography, { variant: "h6", children: "Advanced options" }), _jsx(RadioGroup, { children: Object.entries({
+                                                            single: 'Single',
+                                                            complete: 'Complete',
+                                                        }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: clusterMethod === key, onChange: () => {
+                                                                    setClusterMethod(key);
+                                                                } }), label: val }, key))) })] })) : null] }), results ? (_jsx("div", {})) : loading ? (_jsx(LoadingEllipses, { variant: "h6", title: "Generating genotype matrix" })) : error ? (_jsx(ErrorMessage, { error: error })) : null] }), _jsxs("div", { children: [_jsx(Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "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: {
+                                                classes: {
+                                                    input: classes.textAreaFont,
+                                                },
+                                            },
+                                        } })] })] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                            const { sourcesWithoutLayout } = model;
+                            if (sourcesWithoutLayout) {
+                                try {
+                                    model.setLayout(paste
+                                        .split('\n')
+                                        .map(t => t.trim())
+                                        .filter(f => !!f)
+                                        .map(r => +r)
+                                        .map(idx => {
+                                        const ret = sourcesWithoutLayout[idx - 1];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    getSession(model).notifyError(`${e}`, e);
+                                }
+                            }
+                            handleClose();
+                        }, children: "Apply clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
+});
+export default ClusterDialogManuals;

package/esm/shared/components/ClusterDialog/types.d.ts

@@ -0,0 +1,9 @@
+import type { Source } from '../../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface ReducedModel {
+    sourcesWithoutLayout?: Source[];
+    minorAlleleFrequencyFilter?: number;
+    adapterConfig: AnyConfigurationModel;
+    setLayout: (arg: Source[]) => void;
+    clearLayout: () => void;
+}

package/esm/shared/components/ClusterDialog/types.js

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

package/esm/shared/components/SourcesDataGrid.js

@@ -14,49 +14,56 @@ const useStyles = makeStyles()({
 });
 export default function SourcesDataGrid({ rows, onChange, setSelected, }) {
     const { classes } = useStyles();
-    const { id: _id, name: _name, label: _label, color: _color, baseUri: _baseUri, HP: _HP, ...rest } = rows[0];
     const [currSort, setCurrSort] = useState({
         idx: 0,
         field: null,
     });
-    return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
-                setSelected(arg);
-            }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
-                {
-                    field: 'color',
-                    headerName: 'Color',
-                    renderCell: params => {
-                        const { value, id } = params;
-                        return (_jsx(ColorPicker, { color: value || 'blue', onChange: c => {
-                                const elt = rows.find(f => f.name === id);
-                                if (elt) {
-                                    elt.color = c;
-                                }
-                                onChange([...rows]);
-                            } }));
+    if (rows.length) {
+        const { id: _id, name: _name, label: _label, color: _color, baseUri: _baseUri, HP: _HP, ...rest } = rows[0];
+        return (_jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
+                    setSelected(arg);
+                }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
+                    {
+                        field: 'color',
+                        headerName: 'Color',
+                        renderCell: params => {
+                            const { value, id } = params;
+                            return (_jsx(ColorPicker, { color: value || 'blue', onChange: c => {
+                                    const elt = rows.find(f => f.name === id);
+                                    if (elt) {
+                                        elt.color = c;
+                                    }
+                                    onChange([...rows]);
+                                } }));
+                        },
                     },
-                },
-                {
-                    field: 'label',
-                    headerName: 'Name',
-                    width: measureGridWidth(rows.map(r => r.label)),
-                },
-                ...Object.keys(rest).map(val => ({
-                    field: val,
-                    renderCell: ({ value }) => (_jsx("div", { className: classes.cell, children: _jsx(SanitizedHTML, { html: getStr(value) }) })),
-                    width: measureGridWidth(rows.map(r => `${r[val]}`)),
-                })),
-            ], sortModel: [], onSortModelChange: args => {
-                const sort = args[0];
-                const idx = (currSort.idx + 1) % 2;
-                const field = sort.field || currSort.field;
-                setCurrSort({ idx, field });
-                onChange(field
-                    ? [...rows].sort((a, b) => {
-                        const aa = getStr(a[field]);
-                        const bb = getStr(b[field]);
-                        return idx === 1 ? aa.localeCompare(bb) : bb.localeCompare(aa);
-                    })
-                    : rows);
-            } }) }));
+                    {
+                        field: 'label',
+                        headerName: 'Name',
+                        width: measureGridWidth(rows.map(r => r.label)),
+                    },
+                    ...Object.keys(rest).map(val => ({
+                        field: val,
+                        renderCell: ({ value }) => (_jsx("div", { className: classes.cell, children: _jsx(SanitizedHTML, { html: getStr(value) }) })),
+                        width: measureGridWidth(rows.map(r => `${r[val]}`)),
+                    })),
+                ], sortModel: [], onSortModelChange: args => {
+                    const sort = args[0];
+                    const idx = (currSort.idx + 1) % 2;
+                    const field = sort.field || currSort.field;
+                    setCurrSort({ idx, field });
+                    onChange(field
+                        ? [...rows].sort((a, b) => {
+                            const aa = getStr(a[field]);
+                            const bb = getStr(b[field]);
+                            return idx === 1
+                                ? aa.localeCompare(bb)
+                                : bb.localeCompare(aa);
+                        })
+                        : rows);
+                } }) }));
+    }
+    else {
+        return _jsx("div", { children: "No rows, check sample metadata configuration" });
+    }
 }

package/esm/shared/components/SourcesGridHeader.js

@@ -22,12 +22,12 @@ export default function SourcesGridHeader({ selected, onChange, rows, showTips,
                     onChange(moveDown([...rows], selected, rows.length));
                 }, disabled: !selected.length, children: [_jsx(KeyboardDoubleArrowDownIcon, {}), showTips ? 'Move selected items to bottom' : null] }), _jsx(ColorPopover, { anchorEl: anchorEl, color: widgetColor, onChange: c => {
                     setWidgetColor(c);
-                    selected.forEach(id => {
+                    for (const id of selected) {
                         const elt = rows.find(f => f.name === id);
                         if (elt) {
                             elt.color = c;
                         }
-                    });
+                    }
                     onChange([...rows]);
                 }, onClose: () => {
                     setAnchorEl(null);

package/esm/shared/getSources.d.ts

@@ -0,0 +1,15 @@
+import type { SampleInfo, Source } from './types';
+export declare function getSources({ sources, layout, renderingMode, sampleInfo, }: {
+    sources: Source[];
+    layout?: Source[];
+    renderingMode: string;
+    sampleInfo?: Record<string, SampleInfo>;
+}): {
+    label: string;
+    id: string;
+    baseUri?: string;
+    name: string;
+    color?: string;
+    group?: string;
+    HP?: number;
+}[];

package/esm/shared/getSources.js

@@ -0,0 +1,31 @@
+export function getSources({ sources, layout = sources, renderingMode, sampleInfo, }) {
+    const rows = [];
+    const sourceMap = Object.fromEntries(sources.map(s => [s.name, s]));
+    for (const row of layout) {
+        if (renderingMode === 'phased') {
+            const info = sampleInfo === null || sampleInfo === void 0 ? void 0 : sampleInfo[row.name];
+            if (info === null || info === void 0 ? void 0 : info.isPhased) {
+                const ploidy = info.maxPloidy;
+                for (let i = 0; i < ploidy; i++) {
+                    const id = `${row.name} HP${i}`;
+                    rows.push({
+                        ...sourceMap[row.name],
+                        ...row,
+                        label: id,
+                        HP: i,
+                        id: id,
+                    });
+                }
+            }
+        }
+        else {
+            rows.push({
+                ...sourceMap[row.name],
+                ...row,
+                label: row.name,
+                id: row.name,
+            });
+        }
+    }
+    return rows;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.1.0",
+  "version": "3.2.0",
   "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": "^3.1.0",
-    "@jbrowse/plugin-circular-view": "^3.1.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
-    "@jbrowse/sv-core": "^3.1.0",
+    "@jbrowse/core": "^3.2.0",
+    "@jbrowse/plugin-circular-view": "^3.2.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.2.0",
+    "@jbrowse/sv-core": "^3.2.0",
     "@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": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }

package/dist/shared/components/ClusterDialog.d.ts

@@ -1,11 +0,0 @@
-import type { Source } from '../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function ClusterDialog({ model, handleClose, }: {
-    model: {
-        sources?: Source[];
-        minorAlleleFrequencyFilter?: number;
-        adapterConfig: AnyConfigurationModel;
-        setLayout: (arg: Source[]) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;