@jbrowse/plugin-variants 2.2.1 → 2.3.0

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -4,23 +4,20 @@ import { bytesForRegions } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-import { readConfObject } from '@jbrowse/core/configuration';
+// local
 import VcfFeature from './VcfFeature';
 export default class extends BaseFeatureDataAdapter {
     async configurePre() {
-        const vcfGzLocation = readConfObject(this.config, 'vcfGzLocation');
-        const location = readConfObject(this.config, ['index', 'location']);
-        const indexType = readConfObject(this.config, ['index', 'indexType']);
-        const filehandle = openLocation(vcfGzLocation, this.pluginManager);
+        const pm = this.pluginManager;
+        const vcfGzLocation = this.getConf('vcfGzLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = openLocation(vcfGzLocation, pm);
         const isCSI = indexType === 'CSI';
         const vcf = new TabixIndexedFile({
             filehandle,
-            csiFilehandle: isCSI
-                ? openLocation(location, this.pluginManager)
-                : undefined,
-            tbiFilehandle: !isCSI
-                ? openLocation(location, this.pluginManager)
-                : undefined,
+            csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
+            tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
             chunkCacheSize: 50 * 2 ** 20,
             chunkSizeLimit: 1000000000,
         });

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAMhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAIjC,QAAQ;AACR,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,YAAY,CAAC,aAA6B,EAAE,EAAE,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,UAAU;YACV,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,4BAA4B,CACjC,OAAiB,EACjB,OAAoB,EAAE;QAEtB,OAAO,gBAAgB,CAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,eAAe,CAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,CAAA;YACvD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,IAAI,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACpC,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;YAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;gBACb,yDAAyD;gBACzD,GAAG,GAAG,GAAG,CAAA;aACV;YACD,IAAI,GAAG,GAAG,EAAE,EAAE;gBACZ,OAAO,CAAC,IAAI,CACV,yCAAyC,GAAG,6DAA6D,CAC1G,CAAA;aACF;YACD,KAAK,CAAC,4BAA4B,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACvE,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/esm/VcfTabixAdapter/index.js

@@ -4,6 +4,7 @@ export { default as configSchema } from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfTabixAdapter',
+        displayName: 'VCF tabix adapter',
         configSchema,
         getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
     }));

package/esm/VcfTabixAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAExD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACxE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAExD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,WAAW,EAAE,mBAAmB;QAChC,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACxE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.2.1",
+  "version": "2.3.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/variants",
     "prepublishOnly": "yarn test",
-    "prepack": "yarn build; yarn useDist",
+    "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
@@ -40,7 +40,7 @@
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.2",
-    "@gmod/vcf": "^5.0.5",
+    "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.2",
     "@mui/x-data-grid": "^5.0.1",
     "generic-filehandle": "^3.0.0"
@@ -54,10 +54,9 @@
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
-    "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0",
-    "tss-react": "^3.0.0"
+    "tss-react": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
@@ -65,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
+  "gitHead": "a85b280a8af4d1a11e81ab42913f5f6049e6e580"
 }

package/src/ChordVariantDisplay/index.ts

@@ -10,6 +10,7 @@ export default (pluginManager: PluginManager) => {
     const stateModel = stateModelF(configSchema)
     return new DisplayType({
       name: 'ChordVariantDisplay',
+      displayName: 'Chord variant display',
       configSchema,
       stateModel,
       trackType: 'VariantTrack',

package/src/ChordVariantDisplay/models/stateModelFactory.ts

@@ -46,9 +46,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
           displayModel: self,
           bezierRadius: view.radiusPx * self.bezierRadiusRatio,
           radius: view.radiusPx,
-
-          // @ts-ignore
-          blockDefinitions: this.blockDefinitions,
+          blockDefinitions: self.blockDefinitions,
           config: self.configuration.renderer,
           onChordClick: self.onChordClick,
         }

package/src/LinearVariantDisplay/configSchema.test.js

@@ -48,7 +48,7 @@ test('has a viewType attr', () => {
   )
   const config = configSchema.create({
     type: 'LinearVariantDisplay',
-    displayId: 'diplayId0',
+    displayId: 'displayId0',
     name: 'Zonker Display',
   })
   expect(config.type).toEqual('LinearVariantDisplay')

package/src/LinearVariantDisplay/index.ts

@@ -9,6 +9,7 @@ export default (pluginManager: PluginManager) => {
     const configSchema = configSchemaF(pluginManager)
     return new DisplayType({
       name: 'LinearVariantDisplay',
+      displayName: 'Variant display',
       configSchema,
       stateModel: stateModelFactory(configSchema),
       trackType: 'VariantTrack',

package/src/StructuralVariantChordRenderer/Chord.tsx

@@ -0,0 +1,141 @@
+import React from 'react'
+import { observer } from 'mobx-react'
+import { polarToCartesian, Feature } from '@jbrowse/core/util'
+import {
+  AnyConfigurationModel,
+  readConfObject,
+} from '@jbrowse/core/configuration'
+import { parseBreakend } from '@gmod/vcf'
+
+export interface Region {
+  end: number
+  start: number
+  refName: string
+  elided?: false
+}
+
+export interface ElidedRegion {
+  elided: true
+  regions: Region[]
+}
+
+export type AnyRegion = Region | ElidedRegion
+
+export interface Block {
+  flipped: boolean
+  bpPerRadian: number
+  startRadians: number
+  region: AnyRegion
+}
+
+function bpToRadians(block: Block, pos: number) {
+  const blockStart = block.region.elided ? 0 : block.region.start
+  const blockEnd = block.region.elided ? 0 : block.region.end
+  const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart
+  return bpOffset / block.bpPerRadian + block.startRadians
+}
+
+const Chord = observer(function Chord({
+  feature,
+  blocksForRefs,
+  radius,
+  config,
+  bezierRadius,
+  selected,
+  onClick,
+}: {
+  feature: Feature
+  blocksForRefs: { [key: string]: Block }
+  radius: number
+  config: AnyConfigurationModel
+  bezierRadius: number
+  selected: boolean
+  onClick: (
+    feature: Feature,
+    reg: AnyRegion,
+    endBlock: AnyRegion,
+    evt: unknown,
+  ) => void
+}) {
+  // find the blocks that our start and end points belong to
+  const startBlock = blocksForRefs[feature.get('refName')]
+  if (!startBlock) {
+    return null
+  }
+  let svType
+  if (feature.get('INFO')) {
+    ;[svType] = feature.get('INFO').SVTYPE || []
+  } else if (feature.get('mate')) {
+    svType = 'mate'
+  }
+  let endPosition
+  let endBlock: Block | undefined
+  const alt = feature.get('ALT')?.[0]
+  const bnd = alt && parseBreakend(alt)
+  if (bnd) {
+    // VCF BND
+    const matePosition = bnd.MatePosition.split(':')
+    endPosition = +matePosition[1]
+    endBlock = blocksForRefs[matePosition[0]]
+  } else if (alt === '<TRA>') {
+    // VCF TRA
+    const chr2 = feature.get('INFO')?.CHR2?.[0]
+    const end = feature.get('INFO')?.END?.[0]
+    endPosition = parseInt(end, 10)
+    endBlock = blocksForRefs[chr2]
+  } else if (svType === 'mate') {
+    // generic simplefeatures arcs
+    const mate = feature.get('mate')
+    const chr2 = mate.refName
+    endPosition = mate.start
+    endBlock = blocksForRefs[chr2]
+  }
+
+  if (endBlock) {
+    const startPos = feature.get('start')
+    const startRadians = bpToRadians(startBlock, startPos)
+    const endRadians = bpToRadians(endBlock, endPosition)
+    const startXY = polarToCartesian(radius, startRadians)
+    const endXY = polarToCartesian(radius, endRadians)
+    const controlXY = polarToCartesian(
+      bezierRadius,
+      (endRadians + startRadians) / 2,
+    )
+
+    const strokeColor = selected
+      ? readConfObject(config, 'strokeColorSelected', { feature })
+      : readConfObject(config, 'strokeColor', { feature })
+
+    const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
+      feature,
+    })
+    return (
+      <path
+        data-testid={`chord-${feature.id()}`}
+        d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}
+        style={{ stroke: strokeColor }}
+        onClick={evt => {
+          if (endBlock && startBlock) {
+            onClick(feature, startBlock.region, endBlock.region, evt)
+          }
+        }}
+        onMouseOver={evt => {
+          if (!selected) {
+            evt.currentTarget.style.stroke = hoverStrokeColor
+            evt.currentTarget.style.strokeWidth = '3px'
+          }
+        }}
+        onMouseOut={evt => {
+          if (!selected) {
+            evt.currentTarget.style.stroke = strokeColor
+            evt.currentTarget.style.strokeWidth = '1px'
+          }
+        }}
+      />
+    )
+  }
+
+  return null
+})
+
+export default Chord

package/src/StructuralVariantChordRenderer/ReactComponent.tsx

@@ -1,146 +1,10 @@
 import React, { useMemo } from 'react'
 import { observer } from 'mobx-react'
-import { polarToCartesian, Feature } from '@jbrowse/core/util'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { parseBreakend } from '@gmod/vcf'
+import { Feature } from '@jbrowse/core/util'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
-interface Region {
-  end: number
-  start: number
-  refName: string
-  elided?: false
-}
-
-interface ElidedRegion {
-  elided: true
-  regions: Region[]
-}
-
-type AnyRegion = Region | ElidedRegion
-
-interface Block {
-  flipped: boolean
-  bpPerRadian: number
-  startRadians: number
-  region: AnyRegion
-}
-
-function bpToRadians(block: Block, pos: number) {
-  const blockStart = block.region.elided ? 0 : block.region.start
-  const blockEnd = block.region.elided ? 0 : block.region.end
-  const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart
-  return bpOffset / block.bpPerRadian + block.startRadians
-}
-
-const Chord = observer(function Chord({
-  feature,
-  blocksForRefs,
-  radius,
-  config,
-  bezierRadius,
-  selected,
-  onClick,
-}: {
-  feature: Feature
-  blocksForRefs: { [key: string]: Block }
-  radius: number
-  config: AnyConfigurationModel
-  bezierRadius: number
-  selected: boolean
-  onClick: (
-    feature: Feature,
-    reg: AnyRegion,
-    endBlock: AnyRegion,
-    evt: unknown,
-  ) => void
-}) {
-  // find the blocks that our start and end points belong to
-  const startBlock = blocksForRefs[feature.get('refName')]
-  if (!startBlock) {
-    return null
-  }
-  let svType
-  if (feature.get('INFO')) {
-    ;[svType] = feature.get('INFO').SVTYPE || []
-  } else if (feature.get('mate')) {
-    svType = 'mate'
-  }
-  let endPosition
-  let endBlock: Block | undefined
-  const alt = feature.get('ALT')?.[0]
-  const bnd = alt && parseBreakend(alt)
-  if (bnd) {
-    // VCF BND
-    const matePosition = bnd.MatePosition.split(':')
-    endPosition = +matePosition[1]
-    endBlock = blocksForRefs[matePosition[0]]
-  } else if (alt === '<TRA>') {
-    // VCF TRA
-    const chr2 = feature.get('INFO')?.CHR2?.[0]
-    const end = feature.get('INFO')?.END?.[0]
-    endPosition = parseInt(end, 10)
-    endBlock = blocksForRefs[chr2]
-  } else if (svType === 'mate') {
-    // generic simplefeatures arcs
-    const mate = feature.get('mate')
-    const chr2 = mate.refName
-    endPosition = mate.start
-    endBlock = blocksForRefs[chr2]
-  }
-
-  if (endBlock) {
-    const startPos = feature.get('start')
-    const startRadians = bpToRadians(startBlock, startPos)
-    const endRadians = bpToRadians(endBlock, endPosition)
-    const startXY = polarToCartesian(radius, startRadians)
-    const endXY = polarToCartesian(radius, endRadians)
-    const controlXY = polarToCartesian(
-      bezierRadius,
-      (endRadians + startRadians) / 2,
-    )
-
-    const strokeColor = selected
-      ? readConfObject(config, 'strokeColorSelected', { feature })
-      : readConfObject(config, 'strokeColor', { feature })
-
-    const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
-      feature,
-    })
-    return (
-      <path
-        data-testid={`chord-${feature.id()}`}
-        d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}
-        style={{ stroke: strokeColor }}
-        onClick={evt => {
-          if (endBlock && startBlock) {
-            onClick(feature, startBlock.region, endBlock.region, evt)
-          }
-        }}
-        onMouseOver={evt => {
-          if (!selected) {
-            // @ts-ignore
-            evt.target.style.stroke = hoverStrokeColor
-            // @ts-ignore
-            evt.target.style.strokeWidth = 3
-          }
-        }}
-        onMouseOut={evt => {
-          if (!selected) {
-            // @ts-ignore
-            evt.target.style.stroke = strokeColor
-            // @ts-ignore
-            evt.target.style.strokeWidth = 1
-          }
-        }}
-      />
-    )
-  }
-
-  return null
-})
+// locals
+import Chord, { Block, AnyRegion } from './Chord'
 
 function StructuralVariantChords(props: {
   features: Map<string, Feature>
@@ -170,19 +34,16 @@ function StructuralVariantChords(props: {
   const blocksForRefsMemo = useMemo(() => {
     const blocksForRefs = {} as { [key: string]: Block }
     blockDefinitions.forEach(block => {
-      const regions = block.region.elided
-        ? block.region.regions
-        : [block.region]
-      regions.forEach(region => {
-        blocksForRefs[region.refName] = block
-      })
+      ;(block.region.elided ? block.region.regions : [block.region]).forEach(
+        r => (blocksForRefs[r.refName] = block),
+      )
     })
     return blocksForRefs
   }, [blockDefinitions])
-  // console.log(blocksForRefs)
   const chords = []
-  for (const [id, feature] of features) {
-    const selected = String(selectedFeatureId) === String(feature.id())
+  for (const feature of features.values()) {
+    const id = feature.id()
+    const selected = String(selectedFeatureId) === String(id)
     chords.push(
       <Chord
         key={id}

package/src/StructuralVariantChordRenderer/index.ts

@@ -3,16 +3,15 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import configSchema from './configSchema'
 import ReactComponent from './ReactComponent'
 
-const ChordRendererConfigF = (pluginManager: PluginManager) => {
+export default (pluginManager: PluginManager) => {
   pluginManager.addRendererType(
     () =>
       new ChordRendererType({
         name: 'StructuralVariantChordRenderer',
+        displayName: 'SV chord renderer',
         ReactComponent,
         configSchema,
         pluginManager,
       }),
   )
 }
-
-export default ChordRendererConfigF

package/src/VariantFeatureWidget/BreakendOptionDialog.tsx

@@ -4,30 +4,21 @@ import { observer } from 'mobx-react'
 import {
   Button,
   Checkbox,
-  Dialog,
   DialogActions,
   DialogContent,
-  DialogTitle,
-  Divider,
   FormControlLabel,
-  IconButton,
 } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
-import CloseIcon from '@mui/icons-material/Close'
 import { getSnapshot } from 'mobx-state-tree'
+// jbrowse
+import { Dialog } from '@jbrowse/core/ui'
 import { getSession, Feature } from '@jbrowse/core/util'
 
-const useStyles = makeStyles()(theme => ({
-  closeButton: {
-    position: 'absolute',
-    right: theme.spacing(1),
-    top: theme.spacing(1),
-    color: theme.palette.grey[500],
-  },
+const useStyles = makeStyles()({
   block: {
     display: 'block',
   },
-}))
+})
 
 function BreakendOptionDialog({
   model,
@@ -45,20 +36,7 @@ function BreakendOptionDialog({
   const [mirrorTracks, setMirrorTracks] = useState(true)
 
   return (
-    <Dialog open onClose={handleClose}>
-      <DialogTitle>
-        Breakpoint split view options
-        {handleClose ? (
-          <IconButton
-            className={classes.closeButton}
-            onClick={() => handleClose()}
-          >
-            <CloseIcon />
-          </IconButton>
-        ) : null}
-      </DialogTitle>
-      <Divider />
-
+    <Dialog open onClose={handleClose} title="Breakpoint split view options">
       <DialogContent>
         <FormControlLabel
           className={classes.block}
@@ -92,14 +70,20 @@ function BreakendOptionDialog({
                 feature,
                 view,
               )
+              function remapIds(arr: any[]) {
+                return arr.map((v: any) => ({
+                  ...v,
+                  id: v.trackId + '-' + Math.random(),
+                }))
+              }
               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 viewTracks = getSnapshot(view.tracks) as any
+              viewSnapshot.views[0].tracks = remapIds(viewTracks)
+              viewSnapshot.views[1].tracks = remapIds(
+                mirrorTracks ? viewTracks.slice().reverse() : viewTracks,
+              )
 
               session.addView('BreakpointSplitView', viewSnapshot)
             } catch (e) {

package/src/VariantTrack/index.ts

@@ -8,6 +8,7 @@ export default (pm: PluginManager) => {
     const configSchema = configSchemaF(pm)
     return new TrackType({
       name: 'VariantTrack',
+      displayName: 'Variant track',
       configSchema,
       stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
     })

package/src/VcfAdapter/VcfAdapter.ts

@@ -9,6 +9,8 @@ import { Feature } from '@jbrowse/core/util/simpleFeature'
 import IntervalTree from '@flatten-js/interval-tree'
 import { unzip } from '@gmod/bgzf-filehandle'
 import VCF from '@gmod/vcf'
+
+// local
 import VcfFeature from '../VcfTabixAdapter/VcfFeature'
 
 const readVcf = (f: string) => {

package/src/VcfAdapter/index.ts

@@ -7,6 +7,7 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'VcfAdapter',
+        displayName: 'VCF adapter',
         configSchema,
         getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
       }),

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -14,10 +14,11 @@ import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TabixIndexedFile } from '@gmod/tabix'
 import VcfParser from '@gmod/vcf'
 import { Observer } from 'rxjs'
-import { readConfObject } from '@jbrowse/core/configuration'
-import VcfFeature from './VcfFeature'
 import { GenericFilehandle } from 'generic-filehandle'
 
+// local
+import VcfFeature from './VcfFeature'
+
 export default class extends BaseFeatureDataAdapter {
   private configured?: Promise<{
     filehandle: GenericFilehandle
@@ -26,23 +27,17 @@ export default class extends BaseFeatureDataAdapter {
   }>
 
   private async configurePre() {
-    const vcfGzLocation = readConfObject(this.config, 'vcfGzLocation')
-    const location = readConfObject(this.config, ['index', 'location'])
-    const indexType = readConfObject(this.config, ['index', 'indexType'])
+    const pm = this.pluginManager
+    const vcfGzLocation = this.getConf('vcfGzLocation')
+    const location = this.getConf(['index', 'location'])
+    const indexType = this.getConf(['index', 'indexType'])
 
-    const filehandle = openLocation(
-      vcfGzLocation as FileLocation,
-      this.pluginManager,
-    )
+    const filehandle = openLocation(vcfGzLocation as FileLocation, pm)
     const isCSI = indexType === 'CSI'
     const vcf = new TabixIndexedFile({
       filehandle,
-      csiFilehandle: isCSI
-        ? openLocation(location, this.pluginManager)
-        : undefined,
-      tbiFilehandle: !isCSI
-        ? openLocation(location, this.pluginManager)
-        : undefined,
+      csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
+      tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
       chunkCacheSize: 50 * 2 ** 20,
       chunkSizeLimit: 1000000000,
     })

package/src/VcfTabixAdapter/index.ts

@@ -9,6 +9,7 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'VcfTabixAdapter',
+        displayName: 'VCF tabix adapter',
         configSchema,
         getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
       }),