Rename some files

GMOD · Jan 25, 2025 · b20e4b7 · b20e4b7
1 parent 766f2f1
commit b20e4b7
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Showing 12 changed files with 306 additions and 168 deletions.
diff --git a/plugins/bed/src/BedpeAdapter/BedpeAdapter.ts b/plugins/bed/src/BedpeAdapter/BedpeAdapter.ts
@@ -1,69 +1,14 @@
 import IntervalTree from '@flatten-js/interval-tree'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { SimpleFeature, fetchAndMaybeUnzipText } from '@jbrowse/core/util'
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 
+import { featureData } from './util'
+
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
 import type { Feature, Region } from '@jbrowse/core/util'
 
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL'])
-
-export function featureData(
-  line: string,
-  uniqueId: string,
-  flip: boolean,
-  names?: string[],
-) {
-  const l = line.split('\t')
-  const ref1 = l[flip ? 3 : 0]!
-  const start1 = +l[flip ? 4 : 1]!
-  const end1 = +l[flip ? 5 : 2]!
-  const ref2 = l[!flip ? 3 : 0]!
-  const start2 = +l[!flip ? 4 : 1]!
-  const end2 = +l[!flip ? 5 : 2]!
-  const name = l[6]!
-  const score = +l[7]!
-  const strand1 = parseStrand(l[8]!)
-  const strand2 = parseStrand(l[9]!)
-  const extra = l.slice(10)
-  const rest = names
-    ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-    : {}
-  const ALT = svTypes.has(extra[0]!) ? `<${extra[0]}>` : undefined
-
-  return new SimpleFeature({
-    ...rest,
-    start: start1,
-    end: end1,
-    type: 'paired_feature',
-    refName: ref1,
-    strand: strand1,
-    name,
-    score,
-    uniqueId,
-    mate: {
-      refName: ref2,
-      start: start2,
-      end: end2,
-      strand: strand2,
-    },
-    ...(ALT ? { ALT: [ALT] } : {}), // ALT is an array in VCF
-  })
-}
-
-function parseStrand(strand: string) {
-  if (strand === '+') {
-    return 1
-  } else if (strand === '-') {
-    return -1
-  } else if (strand === '.') {
-    return 0
-  } else {
-    return undefined
-  }
-}
-
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
   protected bedpeFeatures?: Promise<{
     header: string
@@ -81,7 +26,7 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
 
   private async loadDataP(opts?: BaseOptions) {
     const data = await fetchAndMaybeUnzipText(
-      openLocation(this.getConf('bedLoc'), this.pluginManager),
+      openLocation(this.getConf('bedpeLocation'), this.pluginManager),
       opts,
     )
 

diff --git a/plugins/bed/src/BedpeAdapter/util.ts b/plugins/bed/src/BedpeAdapter/util.ts
@@ -0,0 +1,58 @@
+import { SimpleFeature } from '@jbrowse/core/util'
+
+const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL'])
+
+export function featureData(
+  line: string,
+  uniqueId: string,
+  flip: boolean,
+  names?: string[],
+) {
+  const l = line.split('\t')
+  const ref1 = l[flip ? 3 : 0]!
+  const start1 = +l[flip ? 4 : 1]!
+  const end1 = +l[flip ? 5 : 2]!
+  const ref2 = l[!flip ? 3 : 0]!
+  const start2 = +l[!flip ? 4 : 1]!
+  const end2 = +l[!flip ? 5 : 2]!
+  const name = l[6]!
+  const score = +l[7]!
+  const strand1 = parseStrand(l[8]!)
+  const strand2 = parseStrand(l[9]!)
+  const extra = l.slice(10)
+  const rest = names
+    ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
+    : {}
+  const ALT = svTypes.has(extra[0]!) ? `<${extra[0]}>` : undefined
+
+  return new SimpleFeature({
+    ...rest,
+    start: start1,
+    end: end1,
+    type: 'paired_feature',
+    refName: ref1,
+    strand: strand1,
+    name,
+    score,
+    uniqueId,
+    mate: {
+      refName: ref2,
+      start: start2,
+      end: end2,
+      strand: strand2,
+    },
+    ...(ALT ? { ALT: [ALT] } : {}), // ALT is an array in VCF
+  })
+}
+
+function parseStrand(strand: string) {
+  if (strand === '+') {
+    return 1
+  } else if (strand === '-') {
+    return -1
+  } else if (strand === '.') {
+    return 0
+  } else {
+    return undefined
+  }
+}
diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx
@@ -123,7 +123,7 @@ function LaunchBreakpointSplitViewPanel({
   )
 }
 
-export default function BreakendPanel(props: {
+export default function LaunchBreakendPanel(props: {
   locStrings: string[]
   model: VariantFeatureWidgetModel
   feature: SimpleFeatureSerialized

diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendWidgetArea.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendWidgetArea.tsx
@@ -0,0 +1,64 @@
+import { Suspense, lazy } from 'react'
+
+import { parseBreakend } from '@gmod/vcf'
+
+import type { VariantFeatureWidgetModel } from './stateModelFactory'
+
+// lazies
+const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel'))
+
+export default function LaunchBreakendWidgetArea({
+  model,
+}: {
+  model: VariantFeatureWidgetModel
+}) {
+  const { featureData } = model
+  const feat = JSON.parse(JSON.stringify(featureData))
+  const { type = '' } = feat
+
+  return (
+    <Suspense fallback={null}>
+      {type === 'breakend' ? (
+        <LaunchBreakendPanel
+          feature={feat}
+          locStrings={feat.ALT.map(
+            (alt: string) => parseBreakend(alt)?.MatePosition || '',
+          )}
+          model={model}
+        />
+      ) : type === 'translocation' ? (
+        <LaunchBreakendPanel
+          feature={feat}
+          model={model}
+          locStrings={[`${feat.INFO.CHR2[0]}:${feat.INFO.END}`]}
+        />
+      ) : type === 'paired_feature' ? (
+        <LaunchBreakendPanel
+          feature={feat}
+          model={model}
+          locStrings={[`${feat.mate.refName}:${feat.mate.start}`]}
+        />
+      ) : type.includes('inversion') ||
+        type.includes('deletion') ||
+        type.includes('duplication') ||
+        type.includes('cnv') ||
+        type.includes('sv') ? (
+        <LaunchBreakendPanel
+          feature={{
+            uniqueId: 'random',
+            refName: feat.refName,
+            start: feat.start,
+            end: feat.start + 1,
+            mate: {
+              refName: feat.refName,
+              start: feat.end,
+              end: feat.end + 1,
+            },
+          }}
+          model={model}
+          locStrings={[`${feat.refName}:${feat.end}`]}
+        />
+      ) : null}
+    </Suspense>
+  )
+}
diff --git a/plugins/variants/src/VariantFeatureWidget/VariantConsequenceDataGrid.tsx b/plugins/variants/src/VariantFeatureWidget/VariantConsequenceDataGrid.tsx
@@ -0,0 +1,25 @@
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard'
+
+import VariantConsequenceDataGridWrapper from './VariantConsequenceDataGridWrapper'
+
+export default function VariantConsequenceDataGrid({
+  data,
+  fields,
+  title,
+}: {
+  data: string[]
+  fields: string[]
+  title: string
+}) {
+  return data.length ? (
+    <BaseCard title={title}>
+      <VariantConsequenceDataGridWrapper
+        rows={data.map((elt, id) => ({
+          id,
+          ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
+        }))}
+        columns={fields.map(c => ({ field: c }))}
+      />
+    </BaseCard>
+  ) : null
+}
diff --git a/...ts/src/VariantFeatureWidget/AnnotGrid.tsx → ...get/VariantConsequenceDataGridWrapper.tsx b/...ts/src/VariantFeatureWidget/AnnotGrid.tsx → ...get/VariantConsequenceDataGridWrapper.tsx
@@ -6,7 +6,7 @@ import { DataGrid, GridToolbar } from '@mui/x-data-grid'
 
 import type { GridColDef, GridValidRowModel } from '@mui/x-data-grid'
 
-export default function VariantAnnotPanel({
+export default function VariantConsequenceDataGridWrapper({
   rows,
   columns,
 }: {
@@ -33,8 +33,13 @@ export default function VariantAnnotPanel({
       <DataGrid
         rowHeight={25}
         rows={rows}
-        columns={columns.map((c, i) => ({ ...c, width: widths[i] }))}
-        slots={{ toolbar: checked ? GridToolbar : null }}
+        columns={columns.map((c, i) => ({
+          ...c,
+          width: widths[i],
+        }))}
+        slots={{
+          toolbar: checked ? GridToolbar : null,
+        }}
       />
     </div>
   ) : null

diff --git a/...tFeatureWidget/VariantAnnotationTable.tsx → ...FeatureWidget/VariantConsequencePanel.tsx b/...tFeatureWidget/VariantAnnotationTable.tsx → ...FeatureWidget/VariantConsequencePanel.tsx
@@ -1,8 +1,8 @@
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard'
 
-import AnnotGrid from './AnnotGrid'
+import VariantConsequenceDataGridWrapper from './VariantConsequenceDataGridWrapper'
 
-export default function VariantAnnotationTable({
+export default function VariantConsequencePanel({
   data,
   fields,
   title,
@@ -13,7 +13,7 @@ export default function VariantAnnotationTable({
 }) {
   return data.length ? (
     <BaseCard title={title}>
-      <AnnotGrid
+      <VariantConsequenceDataGridWrapper
         rows={data.map((elt, id) => ({
           id,
           ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),