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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,99 +1,96 @@ | ||
| import { parseBreakend } from '@gmod/vcf' | ||
| import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType' | ||
|
|
||
| import { gatherOverlaps } from '@jbrowse/core/util' | ||
| // types | ||
| import type { Assembly } from '@jbrowse/core/assemblyManager/assembly' | ||
| import { | ||
| gatherOverlaps, | ||
| type AbstractSessionModel, | ||
| type Feature, | ||
| } from '@jbrowse/core/util' | ||
| import type { AbstractSessionModel, Feature } from '@jbrowse/core/util' | ||
|
|
||
| export default class BreakpointSplitViewType extends ViewType { | ||
| getBreakendCoveringRegions({ | ||
| feature, | ||
| assembly, | ||
| }: { | ||
| feature: Feature | ||
| assembly: Assembly | ||
| }) { | ||
| const alt = feature.get('ALT')?.[0] | ||
| const bnd = alt ? parseBreakend(alt) : undefined | ||
| const startPos = feature.get('start') | ||
| const refName = feature.get('refName') | ||
| const f = (ref: string) => assembly.getCanonicalRefName(ref) || ref | ||
| export function getBreakendCoveringRegions({ | ||
| feature, | ||
| assembly, | ||
| }: { | ||
| feature: Feature | ||
| assembly: Assembly | ||
| }) { | ||
| const alt = feature.get('ALT')?.[0] | ||
| const bnd = alt ? parseBreakend(alt) : undefined | ||
| const startPos = feature.get('start') | ||
| const refName = feature.get('refName') | ||
| const f = (ref: string) => assembly.getCanonicalRefName(ref) || ref | ||
|
|
||
| if (alt === '<TRA>') { | ||
| const INFO = feature.get('INFO') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(INFO.CHR2[0]), | ||
| matePos: INFO.END[0] - 1, | ||
| } | ||
| } else if (bnd?.MatePosition) { | ||
| const matePosition = bnd.MatePosition.split(':') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(matePosition[0]!), | ||
| matePos: +matePosition[1]! - 1, | ||
| } | ||
| } else if (feature.get('mate')) { | ||
| const mate = feature.get('mate') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(mate.refName), | ||
| matePos: mate.start, | ||
| } | ||
| } else { | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(refName), | ||
| matePos: feature.get('end'), | ||
| } | ||
| if (alt === '<TRA>') { | ||
| const INFO = feature.get('INFO') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(INFO.CHR2[0]), | ||
| matePos: INFO.END[0] - 1, | ||
| } | ||
| } | ||
|
|
||
| singleLevelSnapshotFromBreakendFeature({ | ||
| feature, | ||
| session, | ||
| assemblyName, | ||
| }: { | ||
| feature: Feature | ||
| session: AbstractSessionModel | ||
| assemblyName: string | ||
| }) { | ||
| const { assemblyManager } = session | ||
| const assembly = assemblyManager.get(assemblyName) | ||
| if (!assembly) { | ||
| throw new Error(`assembly ${assemblyName} not found`) | ||
| } else if (bnd?.MatePosition) { | ||
| const matePosition = bnd.MatePosition.split(':') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(matePosition[0]!), | ||
| matePos: +matePosition[1]! - 1, | ||
| } | ||
| if (!assembly.regions) { | ||
| throw new Error(`assembly ${assemblyName} regions not loaded`) | ||
| } else if (feature.get('mate')) { | ||
| const mate = feature.get('mate') | ||
| return { | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(mate.refName), | ||
| matePos: mate.start, | ||
| } | ||
| const coverage = this.getBreakendCoveringRegions({ | ||
| feature, | ||
| assembly, | ||
| }) | ||
| const { refName, mateRefName } = coverage | ||
| const topRegion = assembly.regions.find(f => f.refName === refName)! | ||
| const bottomRegion = assembly.regions.find(f => f.refName === mateRefName)! | ||
| } else { | ||
| return { | ||
| coverage, | ||
| snap: { | ||
| type: 'BreakpointSplitView', | ||
| views: [ | ||
| { | ||
| type: 'LinearGenomeView', | ||
| displayedRegions: gatherOverlaps([topRegion, bottomRegion]), | ||
| }, | ||
| ], | ||
| displayName: `${ | ||
| feature.get('name') || feature.get('id') || 'breakend' | ||
| } split detail`, | ||
| }, | ||
| pos: startPos, | ||
| refName: f(refName), | ||
| mateRefName: f(refName), | ||
| matePos: feature.get('end'), | ||
| } | ||
| } | ||
| } | ||
|
|
||
| export function singleLevelSnapshotFromBreakendFeature({ | ||
| feature, | ||
| session, | ||
| assemblyName, | ||
| }: { | ||
| feature: Feature | ||
| session: AbstractSessionModel | ||
| assemblyName: string | ||
| }) { | ||
| const { assemblyManager } = session | ||
| const assembly = assemblyManager.get(assemblyName) | ||
| if (!assembly) { | ||
| throw new Error(`assembly ${assemblyName} not found`) | ||
| } | ||
| if (!assembly.regions) { | ||
| throw new Error(`assembly ${assemblyName} regions not loaded`) | ||
| } | ||
| const coverage = getBreakendCoveringRegions({ | ||
| feature, | ||
| assembly, | ||
| }) | ||
| const { refName, mateRefName } = coverage | ||
| const topRegion = assembly.regions.find(f => f.refName === refName)! | ||
| const bottomRegion = assembly.regions.find(f => f.refName === mateRefName)! | ||
| return { | ||
| coverage, | ||
| snap: { | ||
| type: 'BreakpointSplitView', | ||
| views: [ | ||
| { | ||
| type: 'LinearGenomeView', | ||
| displayedRegions: gatherOverlaps([ | ||
| { ...topRegion, assemblyName }, | ||
| { ...bottomRegion, assemblyName }, | ||
| ]), | ||
| }, | ||
| ], | ||
| displayName: `${ | ||
| feature.get('name') || feature.get('id') || 'breakend' | ||
| } split detail`, | ||
| }, | ||
| } | ||
| } |
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