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Merge discvr-23.3 to develop
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‎jbrowse/package-lock.json‎

Lines changed: 9508 additions & 12333 deletions
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‎jbrowse/package.json‎

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@@ -11,20 +11,23 @@
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"build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map LK_MODULE_CONTAINER=DiscvrLabKeyModules LK_MODULE=jbrowse webpack --config config/prod.config.js --progress --profile",
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"clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen && rimraf resources/views/browser*",
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"test": "cross-env NODE_ENV=test jest",
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"jb-pkg": "pkg ./node_modules/@jbrowse/cli --out-path ./resources/external/jb-cli"
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"vcffeature-hack": "node ./tools/fixVcfFeature.js",
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"postinstall": "npm run vcffeature-hack",
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"prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli",
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"jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
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},
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"peerDependencies": {
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},
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"dependencies": {
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"@jbrowse/cli": "^1.7.4",
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"@jbrowse/cli": "^2.6.1",
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"@jbrowse/core": "^1.7.4",
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"@jbrowse/plugin-variants": "^1.7.4",
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"@jbrowse/plugin-svg": "^1.7.4",
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"@jbrowse/plugin-linear-genome-view": "^1.7.4",
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"@jbrowse/react-linear-genome-view": "^1.7.4",
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"@labkey/api": "^1.10.0",
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"@labkey/components": "^2.190.0",
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"@labkey/api": "^1.21.0",
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"@labkey/components": "^2.345.0",
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"@gmod/vcf": "^5.0.6",
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"react": "^16.14.0",
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"assert": "^2.0.0",
@@ -35,23 +38,27 @@
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"jspdf-autotable": "^3.5.23",
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"node-polyfill-webpack-plugin": "1.1.4",
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"path-browserify": "^1.0.1",
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"pkg": "^5.3.2",
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"pkg": "^5.8.1",
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"react-data-grid": "^7.0.0-beta.12",
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"react-google-charts": "^3.0.15",
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"react-hot-loader": "^4.13.0",
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"regenerator-runtime": "^0.13.9",
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"stream-browserify": "^3.0.0",
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"typescript": "^3.5.2",
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"typescript": "^4.9.4",
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"util": "^0.12.0",
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"vm-browserify": "^1.1.2",
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"xlsx": "^0.18.3"
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"xlsx": "^0.18.5",
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"fs": "^0.0.1-security",
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"child_process": "^1.0.2",
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"esbuild": "^0.18.4"
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},
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"devDependencies": {
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"@labkey/build": "6.4.0",
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"@labkey/build": "^6.12.0",
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"@types/enzyme": "^3.10.12",
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"@types/jest": "^27.4.1",
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"@types/jquery": "^3.5.14",
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"@types/jexl": "^2.3.0",
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"@types/node": "^18.16.18",
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"enzyme": "^3.11.0",
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"enzyme-adapter-react-16": "^1.15.6",
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"enzyme-to-json": "^3.6.2",

‎jbrowse/src/client/JBrowse/Browser/Browser.tsx‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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import React, { useEffect, useState } from 'react';
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3-
import { JBrowseLinearGenomeView } from '@jbrowse/react-linear-genome-view';
3+
import { JBrowseLinearGenomeView, ViewModel } from '@jbrowse/react-linear-genome-view';
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import { createTheme, makeStyles } from '@material-ui/core/styles';
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import LogSession from './plugins/LogSession/index';
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import ExtendedVariantPlugin from './plugins/ExtendedVariantPlugin/index';
@@ -51,7 +51,7 @@ function View(){
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//TODO: can we make this expand to full page height?
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<div style={{height: "100%"}}>
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<ErrorBoundary>
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<JBrowseLinearGenomeView viewState={state} />
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<JBrowseLinearGenomeView viewState={state as ViewModel} />
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<JBrowseFooter viewState={state} bgColor={bgColor}/>
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</ErrorBoundary>
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</div>

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/ColorWidget.tsx

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@@ -1,17 +1,16 @@
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import {colorSchemes} from "./colorSchemes"
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import {style as styles} from "./style";
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import {getSession} from '@jbrowse/core/util'
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import {readConfObject} from '@jbrowse/core/configuration'
5-
import {generateSchemeJexl} from "./colorUtil";
1+
import { colorSchemes } from './colorSchemes';
2+
import { style as styles } from './style';
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import { getSession } from '@jbrowse/core/util';
4+
import { readConfObject } from '@jbrowse/core/configuration';
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import { generateSchemeJexl } from './colorUtil';
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7-
import {Button, FormControl, InputLabel, MenuItem, Select} from '@material-ui/core'
8-
import {useState} from 'react'
9-
import SchemeTable from './SchemeComponent'
7+
import { Button, FormControl, InputLabel, MenuItem, Select } from '@material-ui/core';
8+
import React, { useState } from 'react';
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import SchemeTable from './SchemeComponent';
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import { SessionWithWidgets } from '@jbrowse/core/util/types';
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import { observer } from 'mobx-react';
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export default jbrowse => {
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const { observer, PropTypes: MobxPropTypes } = jbrowse.jbrequire('mobx-react')
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const React = jbrowse.jbrequire('react')
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function ColorSchemePicker(props){
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const classes = styles()
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const { model } = props
@@ -32,7 +31,8 @@ export default jbrowse => {
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track.displays[0].renderer.palette.set(palette)
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track.displays[0].renderer.color1.set(generateSchemeJexl(palette))
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getSession(model).hideWidget(model)
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const m = getSession(model) as SessionWithWidgets
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m.hideWidget(model)
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}
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const menuItems = (

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/SchemeComponent.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/SchemeComponent.tsx

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@@ -17,7 +17,7 @@ function makeTitle(key){
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const SchemeComponent = observer(props => {
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const classes = styles()
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let scheme = props.scheme
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let scheme = props.scheme as any
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let tableHeader = <></>
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let table = <></>
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const lastRow =
@@ -30,12 +30,11 @@ const SchemeComponent = observer(props => {
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sx={{
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width: 10,
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height: 10,
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backgroundColor: 'gray',
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position: 'relative',
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left: '50%',
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right: '50%'
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}}
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fill='gray'
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bgcolor='gray'
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/>
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</TableCell>
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</TableRow>
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sx={{
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width: 10,
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height: 10,
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backgroundColor: '#'+gradient[i].hex,
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position: 'relative',
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left: '50%',
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right: '50%'
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}}
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fill={'#'+gradient[i].hex}
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bgcolor={'#'+gradient[i].hex}
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/>
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</TableCell>
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</TableRow>)
@@ -96,12 +94,11 @@ const SchemeComponent = observer(props => {
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sx={{
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width: 10,
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height: 10,
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backgroundColor: val,
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position: 'relative',
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left: '50%',
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right: '50%'
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}}
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fill={val}
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bgcolor={val as string}
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/>
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</TableCell>
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</TableRow>

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/colorSchemes.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/colorSchemes.ts

File renamed without changes.

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/colorUtil.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/colorUtil.ts

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@@ -40,7 +40,7 @@ export function generateGradient(hex1, hex2, steps, maxVal){
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}
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export function generateNumJexl(scheme){
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// scheme: an object from colorSchemes.js
43+
// scheme: an object from colorSchemes.ts
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// creates a jexl string that returns colors in a gradient based on schema passed
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let jexl = "jexl"
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let gradientSteps = generateGradient(scheme.options["minVal"], scheme.options["maxVal"], scheme.gradientSteps, scheme.maxVal)
@@ -65,7 +65,7 @@ export function generateNumJexl(scheme){
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}
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export function generateOptJexl(scheme){
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// scheme: an object from colorSchemes.js
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// scheme: an object from colorSchemes.ts
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// creates a jexl string that returns colors based on scheme passed
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let jexl = "jexl"
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Object.entries(scheme.options).map(([key, val]) =>

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/index.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/index.ts

File renamed without changes.

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/style.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ColorWidget/style.ts

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var _styles = require("@material-ui/core/styles")
2-
export const style = (0, _styles.makeStyles)(function (theme) {
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export const style = (_styles.makeStyles)(function (theme) {
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return {
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schemeControl: {
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margin: theme.spacing(2),

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.js renamed to jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/configSchema.ts

File renamed without changes.

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