@jbrowse/plugin-variants 2.18.0 → 3.0.0

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -1,4 +1,5 @@
 import IntervalTree from '@flatten-js/interval-tree';
+import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -7,6 +8,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
     vcfFeatures?: Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     static capabilities: string[];
@@ -14,16 +16,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getMetadata(): Promise<any>;
     setupP(opts?: BaseOptions): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: {
             [k: string]: (sc?: (arg: string) => void) => IntervalTree<any>;
         };
     }>;
     setup(): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+    }[]>;
     freeResources(): void;
 }
 export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,5 +1,5 @@
 import IntervalTree from '@flatten-js/interval-tree';
-import VCF from '@gmod/vcf';
+import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -15,8 +15,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         return header;
     }
     async getMetadata() {
-        const { header } = await this.setup();
-        const parser = new VCF({ header });
+        const { parser } = await this.setup();
         return parser.getMetadata();
     }
     async setupP(opts) {
@@ -29,7 +28,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
-            const n = buffer.indexOf('\n', blockStart);
+            const n = buffer.indexOf(10, blockStart);
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
             const line = decoder.decode(b).trim();
             if (line) {
@@ -51,7 +50,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             blockStart = n + 1;
         }
         const header = headerLines.join('\n');
-        const parser = new VCF({ header });
+        const parser = new VcfParser({ header });
         const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
             refName,
             (sc) => {
@@ -74,6 +73,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         ]));
         return {
             header,
+            parser,
             intervalTreeMap,
         };
     }
@@ -106,6 +106,32 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
+    async getSources() {
+        const conf = this.getConf('samplesTsvLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+            const { parser } = await this.setup();
+            return parser.samples.map(name => ({
+                name,
+            }));
+        }
+        else {
+            const txt = await openLocation(conf).readFile('utf8');
+            const lines = txt.split(/\n|\r\n|\r/);
+            const header = lines[0].split('\t');
+            const { parser } = await this.setup();
+            const s = new Set(parser.samples);
+            return lines
+                .slice(1)
+                .map(line => {
+                const cols = line.split('\t');
+                return {
+                    name: cols[0],
+                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                };
+            })
+                .filter(f => s.has(f.name));
+        }
+    }
     freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];

package/esm/VcfAdapter/configSchema.d.ts

@@ -6,5 +6,13 @@ declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    samplesTsvLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            description: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/esm/VcfAdapter/configSchema.js

@@ -3,7 +3,18 @@ function x() { }
 const VcfAdapter = ConfigurationSchema('VcfAdapter', {
     vcfLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.vcf',
+            locationType: 'UriLocation',
+        },
+    },
+    samplesTsvLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/samples.tsv',
+            description: 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+            locationType: 'UriLocation',
+        },
     },
 }, { explicitlyTyped: true });
 export default VcfAdapter;

package/esm/VcfFeature/index.js

@@ -1,6 +1,6 @@
 import { getSOTermAndDescription } from './util';
 function dataFromVariant(variant, parser) {
-    const { REF = '', ALT, POS, CHROM, ID } = variant;
+    const { FORMAT, REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
     const [type, description] = getSOTermAndDescription(REF, ALT, parser);
     return {
@@ -11,6 +11,7 @@ function dataFromVariant(variant, parser) {
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
         aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
+        format: FORMAT,
     };
 }
 function getEnd(variant) {

package/esm/VcfFeature/util.js

@@ -46,10 +46,9 @@ export function getSOTermAndDescription(ref, alt, parser) {
             return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
         }));
     }
-    if (soTerms.size) {
-        return [[...soTerms].join(','), [...descriptions].join(',')];
-    }
-    return [];
+    return soTerms.size
+        ? [[...soTerms].join(','), [...descriptions].join(',')]
+        : [];
 }
 export function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,24 +1,29 @@
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzipText, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
-    async configurePre() {
-        const pm = this.pluginManager;
+    async configurePre(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const vcfGzLocation = this.getConf('vcfGzLocation');
         const location = this.getConf(['index', 'location']);
         const indexType = this.getConf(['index', 'indexType']);
-        const filehandle = openLocation(vcfGzLocation, pm);
+        const filehandle = openLocation(vcfGzLocation, this.pluginManager);
         const isCSI = indexType === 'CSI';
         const vcf = new TabixIndexedFile({
             filehandle,
-            csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
-            tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
+            csiFilehandle: isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
             chunkCacheSize: 50 * 2 ** 20,
         });
-        const header = await vcf.getHeader();
+        const header = await updateStatus('Downloading index', statusCallback, () => vcf.getHeader());
         return {
             vcf,
             parser: new VcfParser({ header }),
@@ -48,8 +53,9 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { refName, start, end } = query;
+            const { statusCallback = () => { } } = opts;
             const { vcf, parser } = await this.configure();
-            await vcf.getLines(refName, start, end, {
+            await updateStatus('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
                 lineCallback: (line, fileOffset) => {
                     observer.next(new VcfFeature({
                         variant: parser.parseLine(line),
@@ -58,15 +64,35 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
                     }));
                 },
                 ...opts,
-            });
+            }));
             observer.complete();
         }, opts.stopToken);
     }
     async getSources() {
-        const { parser } = await this.configure();
-        return parser.samples.map(name => ({
-            name,
-        }));
+        const conf = this.getConf('samplesTsvLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+            const { parser } = await this.configure();
+            return parser.samples.map(name => ({
+                name,
+            }));
+        }
+        else {
+            const txt = await fetchAndMaybeUnzipText(openLocation(conf, this.pluginManager));
+            const lines = txt.split(/\n|\r\n|\r/);
+            const header = lines[0].split('\t');
+            const { parser } = await this.configure();
+            const s = new Set(parser.samples);
+            return lines
+                .slice(1)
+                .map(line => {
+                const cols = line.split('\t');
+                return {
+                    name: cols[0],
+                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                };
+            })
+                .filter(f => s.has(f.name));
+        }
     }
     freeResources() { }
 }

package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -20,5 +20,13 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    samplesTsvLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            description: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/esm/VcfTabixAdapter/configSchema.js

@@ -20,5 +20,13 @@ const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
             },
         },
     }),
+    samplesTsvLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/samples.tsv',
+            description: 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+            locationType: 'UriLocation',
+        },
+    },
 }, { explicitlyTyped: true });
 export default VcfTabixAdapter;

package/esm/extensionPoints.js

@@ -1,48 +1,36 @@
+import { testAdapter } from '@jbrowse/core/util';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf\.b?gz$/i;
-            const adapterName = 'VcfTabixAdapter';
             const fileName = getFileName(file);
             const indexName = index && getFileName(index);
-            const obj = {
-                type: adapterName,
-                vcfGzLocation: file,
-                index: {
-                    location: index || makeIndex(file, '.tbi'),
-                    indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if (testAdapter(fileName, /\.vcf\.b?gz$/i, adapterHint, 'VcfTabixAdapter')) {
+                return {
+                    type: 'VcfTabixAdapter',
+                    vcfGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if (testAdapter(fileName, /\.vcf(\.gz)?$/i, adapterHint, 'VcfAdapter')) {
+                return {
+                    type: 'VcfAdapter',
+                    vcfLocation: file,
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
         return (adapterName) => {
-            if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
-                return 'VariantTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf$/i;
-            const adapterName = 'VcfAdapter';
-            const fileName = getFileName(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
-                    vcfLocation: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+            return ['VcfTabixAdapter', 'VcfAdapter'].includes(adapterName)
+                ? 'VariantTrack'
+                : trackTypeGuesser(adapterName);
         };
     });
 }

package/esm/getMultiVariantFeaturesAutorun.d.ts

@@ -1,19 +1,16 @@
+import type { SampleInfo, Source } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
-export interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-    [key: string]: string | undefined;
-}
 export declare function getMultiVariantFeaturesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
     sources?: Source[];
-    mafFilter: number;
+    minorAlleleFrequencyFilter: number;
     statsReadyAndRegionNotTooLarge: boolean;
     adapterProps: () => Record<string, unknown>;
     setError: (error: unknown) => void;
     setFeatures: (f: Feature[]) => void;
     setMessage: (str: string) => void;
+    setHasPhased: (arg: boolean) => void;
+    setSampleInfo: (arg: Record<string, SampleInfo>) => void;
 }): void;

package/esm/getMultiVariantFeaturesAutorun.js

@@ -11,25 +11,26 @@ export function getMultiVariantFeaturesAutorun(self) {
                 return;
             }
             const { rpcManager } = getSession(self);
-            const { sources, mafFilter, adapterConfig } = self;
-            if (!sources) {
-                return;
-            }
-            const sessionId = getRpcSessionId(self);
-            const features = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
-                regions: view.dynamicBlocks.contentBlocks,
-                sources,
-                mafFilter,
-                sessionId,
-                adapterConfig,
-            }));
-            if (isAlive(self)) {
-                self.setFeatures(features.map(f => new SimpleFeature(f)));
+            const { sources, minorAlleleFrequencyFilter, adapterConfig } = self;
+            if (sources) {
+                const sessionId = getRpcSessionId(self);
+                const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                if (isAlive(self)) {
+                    self.setHasPhased(hasPhased);
+                    self.setSampleInfo(sampleInfo);
+                    self.setFeatures(features.map(f => new SimpleFeature(f)));
+                }
             }
         }
         catch (e) {
+            console.error(e);
             if (!isAbortException(e) && isAlive(self)) {
-                console.error(e);
                 getSession(self).notifyError(`${e}`, e);
             }
         }

package/esm/getMultiVariantSourcesAutorun.d.ts

@@ -1,10 +1,5 @@
+import type { Source } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-    [key: string]: string | undefined;
-}
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;

package/esm/shared/BulkEditPanel.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { type Source } from '../util';
-export default function BulkEditPanel({ setCurrLayout, currLayout, }: {
+import type { Source } from '../types';
+export default function BulkEditPanel({ onClose, currLayout, }: {
     currLayout: Source[];
-    setCurrLayout: (arg: Source[]) => void;
-}): React.JSX.Element;
+    onClose: (arg?: Source[]) => void;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/shared/BulkEditPanel.js

@@ -1,77 +1,81 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
-import { Button, TextField, Typography } from '@mui/material';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     textAreaFont: {
         fontFamily: 'Courier New',
     },
 });
-export default function BulkEditPanel({ setCurrLayout, currLayout, }) {
+export default function BulkEditPanel({ onClose, currLayout, }) {
     const { classes } = useStyles();
     const [val, setVal] = useState('');
     const [error, setError] = useState();
-    return (React.createElement("div", null,
-        React.createElement(Typography, null, "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no."),
-        React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
-                setVal(event.target.value);
-            }, slotProps: {
-                input: {
-                    classes: {
-                        input: classes.textAreaFont,
-                    },
-                },
-            } }),
-        React.createElement(Button, { variant: "contained", onClick: () => {
-                const lines = val
-                    .split('\n')
-                    .map(f => f.trim())
-                    .filter(f => !!f);
-                const fields = lines[0].split(/[,\t]/gm);
-                if (fields.includes('name')) {
-                    setError('');
-                    const oldLayout = currLayout.map(record => [record.name, record]);
-                    const newData = Object.fromEntries(lines.slice(1).map(line => {
-                        const cols = line.split(/[,\t]/gm);
-                        const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                        return [
-                            newRecord.name,
-                            { ...newRecord, ...oldLayout[newRecord.name] },
-                        ];
-                    }));
-                    setCurrLayout(currLayout.map(record => ({
-                        ...record,
-                        ...newData[record.name],
-                    })));
-                }
-                else {
-                    setError(new Error('No "name" column found on line 1'));
-                }
-            } }, "Update rows"),
-        React.createElement(Button, { variant: "contained", onClick: () => {
-                const lines = val
-                    .split('\n')
-                    .map(f => f.trim())
-                    .filter(f => !!f);
-                const fields = lines[0].split(/[,\t]/gm);
-                if (fields.includes('name')) {
-                    setError('');
-                    const oldLayout = currLayout.map(record => [record.name, record]);
-                    const newData = Object.fromEntries(lines.slice(1).map(line => {
-                        const cols = line.split(/[,\t]/gm);
-                        const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                        return [
-                            newRecord.name,
-                            { ...newRecord, ...oldLayout[newRecord.name] },
-                        ];
-                    }));
-                    setCurrLayout(currLayout.map(record => ({
-                        ...newData[record.name],
-                    })));
-                }
-                else {
-                    setError(new Error('No "name" column found on line 1'));
-                }
-            } }, "Replace rows"),
-        error ? React.createElement(ErrorMessage, { error: error }) : null));
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [_jsx(Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? _jsx(ErrorMessage, { error: error }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
+                            setVal(event.target.value);
+                        }, slotProps: {
+                            input: {
+                                classes: {
+                                    input: classes.textAreaFont,
+                                },
+                            },
+                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...record,
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Update rows" }), _jsx(Button, { variant: "contained", color: "primary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Replace rows" }), _jsx(Button, { variant: "contained", color: "inherit", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
 }

package/esm/shared/ClusterDialog.d.ts

@@ -1,12 +1,11 @@
-import React from 'react';
-import type { Source } from '../util';
+import type { Source } from '../types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function HierarchicalCluster({ model, handleClose, }: {
+export default function ClusterDialog({ model, handleClose, }: {
     model: {
         sources?: Source[];
-        mafFilter?: number;
+        minorAlleleFrequencyFilter?: number;
         adapterConfig: AnyConfigurationModel;
         setLayout: (arg: Source[]) => void;
     };
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;