Fix use of "show all regions with data" feature in SV inspector with …

…TRA entries (with CHR2 from INFO) (#3566)

* Make tests robust to jest --randomize

* Add ability to show all regions with data from TRA features with CHR2

* Update auto-gen docs

plugins/linear-genome-view/src/LinearGenomeView/index.test.ts

@@ -311,7 +311,6 @@ test('can navToMultiple', () => {
 describe('Zoom to selected displayed regions', () => {
   const { Session, LinearGenomeModel } = initialize()
   let model: LGV
-  let largestBpPerPx: number
   beforeEach(() => {
     const session = Session.create({
       configuration: {},
@@ -357,7 +356,6 @@ describe('Zoom to selected displayed regions', () => {
       },
     )
 
-    largestBpPerPx = model.bpPerPx
     expect(model.offsetPx).toEqual(0)
     expect(model.bpPerPx).toBeCloseTo(31.408)
   })
@@ -384,7 +382,6 @@ describe('Zoom to selected displayed regions', () => {
     expect(model.offsetPx).toEqual(0)
     // 10000 - 5000 = 5000 / 800 = 6.25
     expect(model.bpPerPx).toEqual(6.25)
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx)
   })
 
   it('can select one region with start or end outside of displayed region', () => {
@@ -411,7 +408,6 @@ describe('Zoom to selected displayed regions', () => {
     expect(Math.abs(model.offsetPx)).toEqual(0)
     // endOffset 19000 - (-1) = 19001 /  800 = zoomTo(23.75)
     expect(model.bpPerPx).toBeCloseTo(23.75)
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx)
   })
 
   it('can select over two regions in the same reference sequence', () => {
@@ -439,7 +435,6 @@ describe('Zoom to selected displayed regions', () => {
     expect(model.bpPerPx).toBeCloseTo(27.78, 0)
     // offset 5000 / bpPerPx (because that is the starting) = 180.5
     expect(model.offsetPx).toBe(181)
-    expect(model.bpPerPx).toBeLessThan(largestBpPerPx)
   })
 
   it('can navigate to overlapping regions with a region between', () => {

plugins/sv-inspector/src/SvInspectorView/index.ts

@@ -3,10 +3,34 @@ import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 
 import ReactComponent from './components/SvInspectorView'
 import stateModelFactory from './models/SvInspectorView'
+import { Feature, getContainingView, getSession } from '@jbrowse/core/util'
+import { IAnyStateTreeNode } from 'mobx-state-tree'
+
+function defaultOnChordClick(
+  feature: Feature,
+  chordTrack: IAnyStateTreeNode,
+  pluginManager: PluginManager,
+) {
+  const session = getSession(chordTrack)
+  session.setSelection(feature)
+  const view = getContainingView(chordTrack)
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  const viewType = pluginManager.getViewType('BreakpointSplitView') as any
+  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view)
+
+  // try to center the offsetPx
+  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
+  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
+  viewSnapshot.featureData = feature.toJSON()
+
+  session.addView('BreakpointSplitView', viewSnapshot)
+}
 
 export default (pluginManager: PluginManager) => {
+  pluginManager.jexl.addFunction('defaultOnChordClick', defaultOnChordClick)
+
   pluginManager.addViewType(() => {
-    const { stateModel } = stateModelFactory(pluginManager)
+    const stateModel = stateModelFactory(pluginManager)
     return new ViewType({
       name: 'SvInspectorView',
       displayName: 'SV inspector',