MUI data grid replacement + details and genotype link columns (#159)

* Swap out datagrid component for MuiDataGrid

Author: Sebastian Benjamin

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

@@ -1,9 +1,10 @@
 import { observer } from 'mobx-react';
-import { Box, Button } from '@material-ui/core';
+import { Box, Button, ThemeProvider } from '@material-ui/core';
 import React from 'react';
 import HelpDialog from './HelpDialog';
 import { makeStyles } from '@material-ui/core/styles';
-
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { readConfObject } from '@jbrowse/core/configuration';
 
 const useStyles = makeStyles({
     button: {
@@ -29,13 +30,20 @@ const JBrowseFooter = observer(props => {
             <></>
         )
     }
+
+    // This is added to ensure on the first render the buttons use the right color.
+    // NOTE: consider pushing this up one level into Browser.tsx
+    const theme = createJBrowseTheme(readConfObject(viewState.config.configuration, 'theme'))
+
     return (
         <>
-        <Box padding={'5px'}>
-            <Button className={styles.button} onClick={openTrackSelector} variant="contained" color="primary">Open Track Selector</Button>
-            <Button className={styles.button} onClick={showHelpDialog} variant="contained" color="primary">View Help</Button>
-        </Box>
-        <HelpDialog isOpen={dialogOpen} setDialogOpen={setDialogOpen} bgColor={bgColor} />
+        <ThemeProvider theme={theme}>
+            <Box padding={'5px'}>
+                <Button className={styles.button} onClick={openTrackSelector} variant="contained" color="primary">Open Track Selector</Button>
+                <Button className={styles.button} onClick={showHelpDialog} variant="contained" color="primary">View Help</Button>
+            </Box>
+            <HelpDialog isOpen={dialogOpen} setDialogOpen={setDialogOpen} bgColor={bgColor} />
+        </ThemeProvider>
         </>
     )
 })

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts

@@ -1,11 +1,22 @@
 import { VcfFeature } from '@jbrowse/plugin-variants'
+import VcfParser from '@gmod/vcf'
 
 export default class ExtendedVcfFeature extends VcfFeature {
-    constructor(args: { variant: any; parser: any; id: string }) {
+    private readonly vcfParser: VcfParser
+
+    constructor(args: { variant: any; parser: VcfParser; id: string }) {
         args.variant = ExtendedVcfFeature.extractImpact(args.variant)
         //args.variant = ExtendedVcfFeature.calculateVariableSamples(args.variant)
 
-        super(args);
+        super(args)
+
+        this.vcfParser = args.parser
+    }
+
+    public getInfoFieldMeta(propKey: string): VcfParser {
+        const map = this.vcfParser.getMetadata("INFO")
+
+        return map ? map[propKey] :  null
     }
 
     static calculateVariableSamples(variant: {