Misc

plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts

@@ -1,4 +1,9 @@
-import { getSession, Feature, Region } from '@jbrowse/core/util'
+import {
+  getSession,
+  Feature,
+  Region,
+  AbstractSessionModel,
+} from '@jbrowse/core/util'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import { parseBreakend } from '@gmod/vcf'
 import { IStateTreeNode } from 'mobx-state-tree'
@@ -103,15 +108,12 @@ export default class BreakpointSplitViewType extends ViewType {
       featureData: undefined as unknown,
     }
   }
-
-  snapshotFromBreakendFeature(
+  async snapshotFromBreakendFeature(
     feature: Feature,
-    view: { displayedRegions: Region[] } & IStateTreeNode,
+    assemblyName: string,
+    session: AbstractSessionModel,
   ) {
-    const session = getSession(view)
     const bpPerPx = 10
-    const { assemblyName } = view.displayedRegions[0]!
-
     const { assemblyManager } = session
     const assembly = assemblyManager.get(assemblyName)
     if (!assembly) {

plugins/breakpoint-split-view/src/BreakpointSplitView/components/PairedFeatures.tsx

@@ -37,19 +37,17 @@ const PairedFeatures = observer(function ({
   const [mouseoverElt, setMouseoverElt] = useState<string>()
   const snap = getSnapshot(model)
   useNextFrame(snap)
-  const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)
-
-  if (!assembly) {
-    return null
-  }
+  const assembly = views[0]
+    ? assemblyManager.get(views[0].assemblyNames[0]!)
+    : undefined
 
   let yoff = 0
   if (ref.current) {
     const rect = ref.current.getBoundingClientRect()
     yoff = rect.top
   }
 
-  return (
+  return assembly ? (
     <g
       stroke="green"
       strokeWidth={5}
@@ -121,7 +119,7 @@ const PairedFeatures = observer(function ({
         return ret
       })}
     </g>
-  )
+  ) : null
 })
 
 export default PairedFeatures

plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx

@@ -49,7 +49,9 @@ const Translocations = observer(function ({
   const snap = getSnapshot(model)
   useNextFrame(snap)
 
-  const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)
+  const assembly = views[0]
+    ? assemblyManager.get(views[0].assemblyNames[0]!)
+    : undefined
   let yOffset = 0
   if (ref.current) {
     const rect = ref.current.getBoundingClientRect()
@@ -60,7 +62,6 @@ const Translocations = observer(function ({
   // just return null here note: would need to do processing of the INFO
   // CHR2/END and see which view could contain those coordinates to really do
   // it properly
-
   return !assembly || views.length < 2 ? null : (
     <g
       fill="none"
@@ -80,20 +81,18 @@ const Translocations = observer(function ({
           }
 
           const info = f1.get('INFO')
+          const chr1 = f1.get('refName')
           const chr2 = info.CHR2[0]
+          const f1ref = assembly.getCanonicalRefName(chr2) || chr2
+          const f2ref = assembly.getCanonicalRefName(chr1) || chr2
           const end2 = info.END[0]
           const res = info.STRANDS?.[0]?.split('') // not all files have STRANDS
           const [myDirection, mateDirection] = res ?? ['.', '.']
 
-          const r = getPxFromCoordinate(views[level2]!, chr2, end2, assembly)
+          const r = getPxFromCoordinate(views[level2]!, f2ref, end2)
           if (r) {
             const c2: LayoutRecord = [r, 0, r + 1, 0]
-            const x1 = getPxFromCoordinate(
-              views[level1]!,
-              f1.get('refName'),
-              c1[LEFT],
-              assembly,
-            )
+            const x1 = getPxFromCoordinate(views[level1]!, f1ref, c1[LEFT])
             const x2 = r
             const reversed1 = views[level1]!.pxToBp(x1).reversed
             const reversed2 = views[level2]!.pxToBp(x2).reversed

plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts

@@ -4,7 +4,6 @@ import { clamp } from '@jbrowse/core/util'
 
 // locals
 import { LayoutRecord } from './model'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
 type LGV = LinearGenomeViewModel
 
@@ -35,15 +34,10 @@ export function heightFromSpecificLevel(
     : views[level]!.trackRefs[trackId]?.getBoundingClientRect().top || 0
 }
 
-export function getPxFromCoordinate(
-  view: LGV,
-  refName: string,
-  coord: number,
-  asm: Assembly,
-) {
+export function getPxFromCoordinate(view: LGV, refName: string, coord: number) {
   return (
     (view.bpToPx({
-      refName: asm.getCanonicalRefName(refName) || refName,
+      refName,
       coord,
     })?.offsetPx || 0) - view.offsetPx
   )

plugins/spreadsheet-view/src/LaunchSpreadsheetView/index.ts

@@ -16,11 +16,6 @@ export default function LaunchSpreadsheetViewF(pluginManager: PluginManager) {
       uri: string
     }) => {
       const view = session.addView('SpreadsheetView') as SpreadsheetViewModel
-
-      if (!view) {
-        throw new Error('Failed to initialize view')
-      }
-
       view.importWizard.setSelectedAssemblyName(assembly)
       view.importWizard.setSpreadsheetFilehandle({
         uri,

plugins/spreadsheet-view/src/SpreadsheetView/components/ImportWizard.tsx

@@ -45,7 +45,7 @@ const ImportWizard = observer(({ model }: { model: ImportWizardModel }) => {
   const { assemblyNames, assemblyManager } = session
   const { fileTypes, error, loading } = model
   const [selected, setSelected] = useState(assemblyNames[0])
-  const err = assemblyManager.get(selected)?.error || error
+  const err = assemblyManager.get(selected || '')?.error || error
   const rootModel = getRoot<AbstractRootModel>(model)
   const [tmp, setTmp] = useState<FileLocation>()
   const [fileType, setFileType] = useState(getFileType(tmp))

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts

@@ -13,9 +13,9 @@ export async function parseBedBuffer(buffer: Buffer) {
   for (
     ;
     i < lines.length &&
-    (lines[i].startsWith('#') ||
-      lines[i].startsWith('browser') ||
-      lines[i].startsWith('track'));
+    (lines[i]!.startsWith('#') ||
+      lines[i]!.startsWith('browser') ||
+      lines[i]!.startsWith('track'));
     i++
   ) {
     headerLines.push(lines[i])
@@ -45,13 +45,13 @@ export async function parseBedBuffer(buffer: Buffer) {
   ])
   const rows = []
   for (let j = 0; i < lines.length; i++, j++) {
-    const line = lines[i]
+    const line = lines[i]!
     const l = line.split('\t')
-    const refName = l[0]
-    const start = +l[1]
-    const end = +l[2]
-    const name = l[3]
-    const score = +l[4]
+    const refName = l[0]!
+    const start = +l[1]!
+    const end = +l[2]!
+    const name = l[3]!
+    const score = +l[4]!
     const strand = parseStrand(l[5])
 
     const extra = l.slice(MAX_BED_COL)

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts

@@ -11,9 +11,9 @@ export async function parseBedPEBuffer(buffer: Buffer) {
   for (
     ;
     i < lines.length &&
-    (lines[i].startsWith('#') ||
-      lines[i].startsWith('browser') ||
-      lines[i].startsWith('track'));
+    (lines[i]!.startsWith('#') ||
+      lines[i]!.startsWith('browser') ||
+      lines[i]!.startsWith('track'));
     i++
   ) {
     headerLines.push(lines[i])
@@ -43,22 +43,22 @@ export async function parseBedPEBuffer(buffer: Buffer) {
   ])
   const rows = []
   for (let j = 0; i < lines.length; i++, j++) {
-    const line = lines[i]
+    const line = lines[i]!
     const l = line.split('\t')
-    const ref1 = l[0]
-    const start1 = +l[1]
-    const end1 = +l[2]
-    const ref2 = l[3]
-    const start2 = +l[4]
-    const end2 = +l[5]
-    const name = l[6]
-    const score = +l[7]
+    const ref1 = l[0]!
+    const start1 = +l[1]!
+    const end1 = +l[2]!
+    const ref2 = l[3]!
+    const start2 = +l[4]!
+    const end2 = +l[5]!
+    const name = l[6]!
+    const score = +l[7]!
     const strand1 = parseStrand(l[8])
     const strand2 = parseStrand(l[9])
 
     let extra = l.slice(MAX_BEDPE_COL)
-    let ALT
-    if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])) {
+    let ALT: string | undefined
+    if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0] || '')) {
       ALT = `<${extra[0]}>`
       if (j < MAX_SET_SCAN) {
         columns.add('ALT')

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts

@@ -1,7 +1,7 @@
 export function parseSTARFusionBuffer(buffer: Buffer) {
   const str = new TextDecoder('utf8').decode(buffer)
   const lines = str.split(/\n|\r\n/)
-  const header = lines[0].slice(1).split('\t')
+  const header = lines[0]?.slice(1).split('\t') || []
   return {
     rows: lines
       .slice(1)

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts

@@ -10,7 +10,7 @@ function getRows(lines: string[], vcfParser: VCF) {
         .map(f => f.trim())
         .map(e => {
           const [key, val = 'true'] = e.split('=')
-          const k = `INFO.${key.trim()}`
+          const k = `INFO.${key!.trim()}`
           keys.add(k)
           return [k, val.trim()]
         }) || [],
@@ -45,7 +45,7 @@ export function parseVcfBuffer(buffer: Buffer) {
     .filter(f => !!f)
   const headerLines = []
   let i = 0
-  for (; i < lines.length && lines[i].startsWith('#'); i++) {
+  for (; i < lines.length && lines[i]!.startsWith('#'); i++) {
     headerLines.push(lines[i])
   }
   const header = headerLines.join('\n')

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts

@@ -12,7 +12,7 @@ import VCF, { parseBreakend } from '@gmod/vcf'
 import { locationLinkClick } from '../components/util'
 import { SpreadsheetModel } from '../models/Spreadsheet'
 
-export function parseStrand(strand: string) {
+export function parseStrand(strand?: string) {
   if (strand === '+') {
     return 1
   } else if (strand === '-') {
@@ -83,8 +83,8 @@ function getBreakpoints(feature: Feature) {
   const alt = feature.get('ALT')?.[0]
 
   const bnd = alt ? parseBreakend(alt) : undefined
-  let endPos
-  let mateRefName: string | undefined
+  let endPos: number
+  let mateRefName: string
 
   // a VCF breakend feature
   if (alt === '<TRA>') {
@@ -93,12 +93,14 @@ function getBreakpoints(feature: Feature) {
     mateRefName = INFO.CHR2[0]
   } else if (bnd?.MatePosition) {
     const matePosition = bnd.MatePosition.split(':')
-    endPos = +matePosition[1] - 1
-    mateRefName = matePosition[0]
+    endPos = +matePosition[1]! - 1
+    mateRefName = matePosition[0]!
   } else if (feature.get('mate')) {
     const mate = feature.get('mate')
     mateRefName = mate.refName
     endPos = mate.start
+  } else {
+    throw new Error('unknown mate')
   }
 
   return [

plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts

@@ -8,7 +8,6 @@ import {
 import { GenericFilehandle } from 'generic-filehandle'
 
 // locals
-import { SpreadsheetViewStateModel } from './SpreadsheetView'
 import { autorun } from 'mobx'
 import { getFileType, getFilename } from '../components/util'
 
@@ -143,10 +142,6 @@ function stateModelFactory() {
                 self.fileType as keyof typeof fileTypeParsers
               ]()
 
-            if (!typeParser) {
-              throw new Error(`cannot open files of type '${self.fileType}'`)
-            }
-
             const { unzip } = await import('@gmod/bgzf-filehandle')
             const { pluginManager } = getEnv(self)
             const f = openLocation(spreadsheetFilehandle, pluginManager)
@@ -162,7 +157,7 @@ function stateModelFactory() {
               const buffer = await f.readFile()
               const buf2 = self.requiresUnzip ? await unzip(buffer) : buffer
               const spreadsheet = await typeParser(buf2)
-              getParent<SpreadsheetViewStateModel>(self).displaySpreadsheet(
+              getParent<any>(self).displaySpreadsheet(
                 spreadsheet,
                 self.selectedAssemblyName,
               )

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

@@ -15,13 +15,7 @@ export default function LaunchSvInspectorViewF(pluginManager: PluginManager) {
       assembly: string
       uri: string
     }) => {
-      // add view, make typescript happy with return type
       const view = session.addView('SvInspectorView') as SvInspectorViewModel
-
-      if (!view) {
-        throw new Error('Failed to initialize view')
-      }
-
       view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly)
       view.spreadsheetView.importWizard.setSpreadsheetFilehandle({
         uri,

plugins/sv-inspector/src/SvInspectorView/components/SvInspectorView.tsx

@@ -61,6 +61,7 @@ const SvInspectorView = observer(function ({
           onDrag={(_, total) => {
             circularView.setWidth(initialCircWidth + total)
             spreadsheetView.setWidth(initialSpreadsheetWidth - total)
+            return undefined
           }}
           onMouseDown={() => {
             setInitialSpreadsheetWidth(spreadsheetView.width)

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

@@ -20,6 +20,9 @@ async function defaultOnChordClick(
     'BreakpointSplitView',
   ) as BreakpointSplitViewType
   const [assemblyName] = view.assemblyNames
+  if (!assemblyName) {
+    throw new Error('error trying to understand what assembly to use')
+  }
   const viewSnapshot = await viewType.snapshotFromBreakendFeature(
     feature,
     assemblyName,

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

@@ -154,7 +154,8 @@ function SvInspectorViewF(pluginManager: PluginManager) {
             {
               type: 'ChordVariantDisplay',
               displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
-              onChordClick: `jexl:defaultOnChordClick(feature, track, pluginManager)`,
+              onChordClick:
+                'jexl:defaultOnChordClick(feature, track, pluginManager)',
               renderer: {
                 type: 'StructuralVariantChordRenderer',
               },
@@ -308,7 +309,7 @@ function SvInspectorViewF(pluginManager: PluginManager) {
               circularView.hideTrack(t.configuration.trackId),
             )
             // put our track in as the only track
-            if (assemblyName && featuresCircularTrackConfiguration) {
+            if (assemblyName) {
               circularView.addTrackConf(featuresCircularTrackConfiguration)
             }
           }),