Reduce self-pairing for some paired-end read data in breakpoint split…

… view (#4667)
GMOD · Nov 19, 2024 · 9a83551 · 9a83551
1 parent 1cccc87
commit 9a83551
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Showing 4 changed files with 1,012 additions and 952 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -130,6 +130,7 @@ export default tseslint.config(
       'unicorn/prefer-at': 'off',
       'unicorn/prefer-string-replace-all': 'off',
       'unicorn/no-array-reduce': 'off',
+      'unicorn/expiring-todo-comments': 'off',
 
       '@typescript-eslint/no-deprecated': 'off',
       '@typescript-eslint/no-explicit-any': 'off',

diff --git a/...ents/src/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.tsx b/...ents/src/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.tsx
@@ -30,7 +30,6 @@ export default function LaunchBreakpointSplitViewPanel({
   feature: SimpleFeatureSerialized
   viewType: ViewType
 }) {
-  const session = getSession(model)
   const { view } = model
   const [res, setRes] = useState<ReducedFeature[]>()
   const [error, setError] = useState<unknown>()
@@ -67,50 +66,92 @@ export default function LaunchBreakpointSplitViewPanel({
             <li key={`${JSON.stringify(arg)}-${index}`}>
               {f1.refName}:{toLocale(f1.strand === 1 ? f1.end : f1.start)} -&gt;{' '}
               {f2.refName}:{toLocale(f2.strand === 1 ? f2.start : f2.end)}{' '}
-              <Link
-                href="#"
-                onClick={event => {
-                  event.preventDefault()
-                  session.queueDialog(handleClose => [
-                    BreakendMultiLevelOptionDialog,
-                    {
-                      handleClose,
-                      model,
-                      feature: new SimpleFeature({ ...f1, mate: f2 }),
-                      // @ts-expect-error
-                      viewType,
-                      view: model.view,
-                      assemblyName: model.view.displayedRegions[0].assemblyName,
-                    },
-                  ])
-                }}
-              >
-                (top/bottom)
-              </Link>{' '}
-              <Link
-                href="#"
-                onClick={event => {
-                  event.preventDefault()
-                  session.queueDialog(handleClose => [
-                    BreakendSingleLevelOptionDialog,
-                    {
-                      handleClose,
-                      model,
-                      feature: new SimpleFeature({ ...f1, mate: f2 }),
-                      // @ts-expect-error
-                      viewType,
-                      view: model.view,
-                      assemblyName: model.view.displayedRegions[0].assemblyName,
-                    },
-                  ])
-                }}
-              >
-                (single row)
-              </Link>
+              <TopBottomSplitViewLink
+                model={model}
+                f1={f1}
+                f2={f2}
+                viewType={viewType}
+              />{' '}
+              <SideBySideViewLink
+                model={model}
+                f1={f1}
+                f2={f2}
+                viewType={viewType}
+              />
             </li>
           )
         })}
       </ul>
     </div>
   ) : null
 }
+
+function TopBottomSplitViewLink({
+  model,
+  f1,
+  f2,
+  viewType,
+}: {
+  model: AlignmentFeatureWidgetModel
+  f1: ReducedFeature
+  f2: ReducedFeature
+  viewType: ViewType
+}) {
+  return (
+    <Link
+      href="#"
+      onClick={event => {
+        event.preventDefault()
+        getSession(model).queueDialog(handleClose => [
+          BreakendMultiLevelOptionDialog,
+          {
+            handleClose,
+            model,
+            feature: new SimpleFeature({ ...f1, mate: f2 }),
+            // @ts-expect-error
+            viewType,
+            view: model.view,
+            assemblyName: model.view.displayedRegions[0].assemblyName,
+          },
+        ])
+      }}
+    >
+      (top/bottom)
+    </Link>
+  )
+}
+
+function SideBySideViewLink({
+  model,
+  f1,
+  f2,
+  viewType,
+}: {
+  model: AlignmentFeatureWidgetModel
+  f1: ReducedFeature
+  f2: ReducedFeature
+  viewType: ViewType
+}) {
+  return (
+    <Link
+      href="#"
+      onClick={event => {
+        event.preventDefault()
+        getSession(model).queueDialog(handleClose => [
+          BreakendSingleLevelOptionDialog,
+          {
+            handleClose,
+            model,
+            feature: new SimpleFeature({ ...f1, mate: f2 }),
+            // @ts-expect-error
+            viewType,
+            view: model.view,
+            assemblyName: model.view.displayedRegions[0].assemblyName,
+          },
+        ])
+      }}
+    >
+      (single row)
+    </Link>
+  )
+}
diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/util.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/util.ts
@@ -1,4 +1,4 @@
-import { Feature, notEmpty } from '@jbrowse/core/util'
+import { assembleLocStringFast, Feature, notEmpty } from '@jbrowse/core/util'
 
 import { parseBreakend } from '@gmod/vcf'
 
@@ -7,15 +7,26 @@ import { parseBreakend } from '@gmod/vcf'
 export function getBadlyPairedAlignments(features: Map<string, Feature>) {
   const candidates = new Map<string, Feature[]>()
   const alreadySeen = new Set<string>()
+  const alreadyPairedWithSamePosition = new Set<string>()
 
   // this finds candidate features that share the same name
   for (const feature of features.values()) {
     const flags = feature.get('flags')
     const id = feature.id()
+    const supp = assembleLocStringFast({
+      refName: feature.get('refName'),
+      start: feature.get('start'),
+      end: feature.get('end'),
+    })
     const unmapped = flags & 4
     const correctlyPaired = flags & 2
 
-    if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) {
+    if (
+      !alreadySeen.has(id) &&
+      !alreadyPairedWithSamePosition.has(supp) &&
+      !correctlyPaired &&
+      !unmapped
+    ) {
       const n = feature.get('name')
       let val = candidates.get(n)
       if (!val) {
@@ -25,6 +36,7 @@ export function getBadlyPairedAlignments(features: Map<string, Feature>) {
       val.push(feature)
     }
     alreadySeen.add(feature.id())
+    alreadyPairedWithSamePosition.add(supp)
   }
 
   return [...candidates.values()].filter(v => v.length > 1)