Misc

plugins/arc/src/LinearPairedArcDisplay/components/Arcs.tsx

@@ -13,80 +13,7 @@ import { getConf } from '@jbrowse/core/configuration'
 // local
 import { LinearArcDisplayModel } from '../model'
 import ArcTooltip from '../../ArcTooltip'
-
-export function makeFeaturePair(feature: Feature, alt?: string) {
-  const bnd = alt ? parseBreakend(alt) : undefined
-  let start = feature.get('start')
-  let end = feature.get('end')
-  const strand = feature.get('strand')
-  const mate = feature.get('mate') as {
-    refName: string
-    start: number
-    end: number
-    mateDirection?: number
-  }
-  const refName = feature.get('refName')
-
-  let mateRefName: string | undefined
-  let mateEnd = 0
-  let mateStart = 0
-  let joinDirection = 0
-  let mateDirection = 0
-
-  // one sided bracket used, because there could be <INS:ME> and we just check
-  // startswith below
-  const symbolicAlleles = ['<TRA', '<DEL', '<INV', '<INS', '<DUP', '<CNV']
-  if (symbolicAlleles.some(a => alt?.startsWith(a))) {
-    // END is defined to be a single value, not an array. CHR2 not defined in
-    // VCF spec, but should be similar
-    const info = feature.get('INFO')
-    const e = info?.END?.[0] ?? end
-    mateRefName = info?.CHR2?.[0] ?? refName
-    mateEnd = e
-    mateStart = e - 1
-    // re-adjust the arc to be from start to end of feature by re-assigning end
-    // to the 'mate'
-    start = start
-    end = start + 1
-  } else if (bnd?.MatePosition) {
-    const matePosition = bnd.MatePosition.split(':')
-    mateDirection = bnd.MateDirection === 'left' ? 1 : -1
-    joinDirection = bnd.Join === 'left' ? -1 : 1
-    mateEnd = +matePosition[1]
-    mateStart = +matePosition[1] - 1
-    mateRefName = matePosition[0]
-  }
-
-  return {
-    k1: {
-      refName,
-      start,
-      end,
-      strand,
-      mateDirection,
-    },
-    k2: mate ?? {
-      refName: mateRefName,
-      end: mateEnd,
-      start: mateStart,
-      mateDirection: joinDirection,
-    },
-  }
-}
-
-export function makeSummary(feature: Feature, alt?: string) {
-  const { k1, k2 } = makeFeaturePair(feature, alt)
-  return [
-    feature.get('name'),
-    feature.get('id'),
-    assembleLocString(k1),
-    assembleLocString(k2),
-    feature.get('INFO')?.SVTYPE,
-    alt,
-  ]
-    .filter(f => !!f)
-    .join(' - ')
-}
+import { makeFeaturePair, makeSummary } from './util'
 
 type LGV = LinearGenomeViewModel
 

plugins/arc/src/LinearPairedArcDisplay/components/util.ts

@@ -0,0 +1,75 @@
+import { parseBreakend } from '@gmod/vcf'
+import { Feature, assembleLocString } from '@jbrowse/core/util'
+export function makeFeaturePair(feature: Feature, alt?: string) {
+  const bnd = alt ? parseBreakend(alt) : undefined
+  let start = feature.get('start')
+  let end = feature.get('end')
+  const strand = feature.get('strand')
+  const mate = feature.get('mate') as {
+    refName: string
+    start: number
+    end: number
+    mateDirection?: number
+  }
+  const refName = feature.get('refName')
+
+  let mateRefName: string | undefined
+  let mateEnd = 0
+  let mateStart = 0
+  let joinDirection = 0
+  let mateDirection = 0
+
+  // one sided bracket used, because there could be <INS:ME> and we just check
+  // startswith below
+  const symbolicAlleles = ['<TRA', '<DEL', '<INV', '<INS', '<DUP', '<CNV']
+  if (symbolicAlleles.some(a => alt?.startsWith(a))) {
+    // END is defined to be a single value, not an array. CHR2 not defined in
+    // VCF spec, but should be similar
+    const info = feature.get('INFO')
+    const e = info?.END?.[0] ?? end
+    mateRefName = info?.CHR2?.[0] ?? refName
+    mateEnd = e
+    mateStart = e - 1
+    // re-adjust the arc to be from start to end of feature by re-assigning end
+    // to the 'mate'
+    start = start
+    end = start + 1
+  } else if (bnd?.MatePosition) {
+    const matePosition = bnd.MatePosition.split(':')
+    mateDirection = bnd.MateDirection === 'left' ? 1 : -1
+    joinDirection = bnd.Join === 'left' ? -1 : 1
+    mateEnd = +matePosition[1]
+    mateStart = +matePosition[1] - 1
+    mateRefName = matePosition[0]
+  }
+
+  return {
+    k1: {
+      refName,
+      start,
+      end,
+      strand,
+      mateDirection,
+    },
+    k2: mate ?? {
+      refName: mateRefName,
+      end: mateEnd,
+      start: mateStart,
+      mateDirection: joinDirection,
+    },
+  }
+}
+
+export function makeSummary(feature: Feature, alt?: string) {
+  const { k1, k2 } = makeFeaturePair(feature, alt)
+  return [
+    feature.get('name'),
+    feature.get('id'),
+    assembleLocString(k1),
+    assembleLocString(k2),
+    feature.get('INFO')?.SVTYPE,
+    alt,
+  ]
+    .filter(f => !!f)
+    .join(' - ')
+}