@jbrowse/plugin-variants 1.6.4 → 1.6.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.6.4",
+  "version": "1.6.7",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^1.4.2",
+    "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.2",
     "@gmod/vcf": "^5.0.5",
     "@material-ui/icons": "^4.11.2",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "7f157fbb2302d8825f99d01bcc0fd0616116c5d2"
+  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
 }

package/src/VariantFeatureWidget/BreakendOptionDialog.tsx

@@ -1,7 +1,6 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import React, { useState } from 'react'
 import { observer } from 'mobx-react'
-import { makeStyles } from '@material-ui/core/styles'
 import {
   Button,
   Dialog,
@@ -12,6 +11,7 @@ import {
   IconButton,
   FormControlLabel,
   Checkbox,
+  makeStyles,
 } from '@material-ui/core'
 import CloseIcon from '@material-ui/icons/Close'
 import { getSnapshot } from 'mobx-state-tree'
@@ -52,9 +52,7 @@ function BreakendOptionDialog({
         {handleClose ? (
           <IconButton
             className={classes.closeButton}
-            onClick={() => {
-              handleClose()
-            }}
+            onClick={() => handleClose()}
           >
             <CloseIcon />
           </IconButton>
@@ -90,22 +88,25 @@ function BreakendOptionDialog({
           onClick={() => {
             const { view } = model
             const session = getSession(model)
+            try {
+              const viewSnapshot = viewType.snapshotFromBreakendFeature(
+                feature,
+                view,
+              )
+              viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
+              viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
+              viewSnapshot.featureData = feature
+              const viewTracks: any = getSnapshot(view.tracks)
+              viewSnapshot.views[0].tracks = viewTracks
+              viewSnapshot.views[1].tracks = mirrorTracks
+                ? viewTracks.slice().reverse()
+                : viewTracks
 
-            const viewSnapshot = viewType.snapshotFromBreakendFeature(
-              feature,
-              view,
-            )
-            viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
-            viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
-            viewSnapshot.featureData = feature
-            const viewTracks: any = getSnapshot(view.tracks)
-            viewSnapshot.views[0].tracks = viewTracks
-            viewSnapshot.views[1].tracks = mirrorTracks
-              ? viewTracks.slice().reverse()
-              : viewTracks
-
-            session.addView('BreakpointSplitView', viewSnapshot)
-
+              session.addView('BreakpointSplitView', viewSnapshot)
+            } catch (e) {
+              console.error(e)
+              session.notify(`${e}`)
+            }
             handleClose()
           }}
           variant="contained"
@@ -115,12 +116,9 @@ function BreakendOptionDialog({
           OK
         </Button>
         <Button
-          onClick={() => {
-            handleClose()
-          }}
+          onClick={() => handleClose()}
           color="secondary"
           variant="contained"
-          autoFocus
         >
           Cancel
         </Button>

package/src/VariantFeatureWidget/VariantFeatureWidget.tsx

@@ -146,13 +146,17 @@ function BreakendPanel(props: {
               onClick={(event: any) => {
                 event.preventDefault()
                 const { view } = model
-                if (view) {
-                  view.navToLocString?.(locString)
-                } else {
-                  session.notify(
-                    'No view associated with this feature detail panel anymore',
-                    'warning',
-                  )
+                try {
+                  if (view) {
+                    view.navToLocString?.(locString)
+                  } else {
+                    throw new Error(
+                      'No view associated with this feature detail panel anymore',
+                    )
+                  }
+                } catch (e) {
+                  console.error(e)
+                  session.notify(`${e}`)
                 }
               }}
             >

package/src/index.ts

@@ -78,7 +78,10 @@ export default class VariantsPlugin extends Plugin {
       'Core-guessTrackTypeForLocation',
       (trackTypeGuesser: TrackTypeGuesser) => {
         return (adapterName: string) => {
-          if (adapterName === 'VcfTabixAdapter') {
+          if (
+            adapterName === 'VcfTabixAdapter' ||
+            adapterName === 'VcfAdapter'
+          ) {
             return 'VariantTrack'
           }
           return trackTypeGuesser(adapterName)