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Create features for single-row breakpoint split view rendering of deletions, inversions, etc. (#4561)
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‎component_tests/cgv/package.json

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@@ -42,6 +42,7 @@
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"@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
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"@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
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"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
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"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
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"@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
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"@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz",
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"@jbrowse/react-circular-genome-view": "file:./packed/jbrowse-react-circular-genome-view.tgz"

‎component_tests/lgv/package.json

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"@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
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"@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
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"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
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"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
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"@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
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"@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz"
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},

‎component_tests/react-app/package.json

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@@ -55,6 +55,7 @@
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"@jbrowse/plugin-spreadsheet-view": "file:./packed/jbrowse-plugin-spreadsheet-view.tgz",
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"@jbrowse/plugin-sv-inspector": "file:./packed/jbrowse-plugin-sv-inspector.tgz",
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"@jbrowse/app-core": "file:./packed/jbrowse-app-core.tgz",
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"@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
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"@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
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"@jbrowse/web-core": "file:./packed/jbrowse-web-core.tgz"
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},

‎packages/core/BaseFeatureWidget/BaseFeatureDetail/util.ts

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@@ -7,7 +7,7 @@ export function isEmpty(obj: Record<string, unknown>) {
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}
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export function generateTitle(name: unknown, id: unknown, type: unknown) {
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return [ellipses(`${name}` || `${id}`), `${type}`]
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return [ellipses(`${name || id || ''}`), `${type}`]
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.filter(f => !!f)
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.join(' - ')
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}

‎packages/core/util/index.ts

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@@ -1369,14 +1369,14 @@ export function mergeIntervals<T extends { start: number; end: number }>(
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return intervals
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}
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1372-
const stack = []
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const stack = [] as T[]
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let top = null
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// sort the intervals based on their start values
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intervals = intervals.sort((a, b) => a.start - b.start)
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// push the 1st interval into the stack
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stack.push(intervals[0])
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stack.push(intervals[0]!)
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// start from the next interval and merge if needed
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for (let i = 1; i < intervals.length; i++) {
@@ -1404,13 +1404,12 @@ interface BasicFeature {
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end: number
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start: number
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refName: string
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assemblyName?: string
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}
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1409-
// hashmap of refName->array of features
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type FeaturesPerRef = Record<string, BasicFeature[]>
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1412-
export function gatherOverlaps(regions: BasicFeature[]) {
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const memo = {} as FeaturesPerRef
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// returns new array non-overlapping features
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export function gatherOverlaps(regions: BasicFeature[], w = 5000) {
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const memo = {} as Record<string, BasicFeature[]>
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for (const x of regions) {
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if (!memo[x.refName]) {
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memo[x.refName] = []
@@ -1419,7 +1418,10 @@ export function gatherOverlaps(regions: BasicFeature[]) {
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}
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14211420
return Object.values(memo).flatMap(group =>
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mergeIntervals(group.sort((a, b) => a.start - b.start)),
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mergeIntervals(
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group.sort((a, b) => a.start - b.start),
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w,
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),
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)
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}
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‎packages/sv-core/package.json

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{
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"name": "@jbrowse/sv-core",
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"version": "2.15.0",
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"description": "JBrowse 2 code shared between sv type code",
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"keywords": [
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"jbrowse",
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"jbrowse2",
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"bionode",
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"biojs",
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"genomics"
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],
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"license": "Apache-2.0",
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"homepage": "https://jbrowse.org",
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"bugs": "https://github.com/GMOD/jbrowse-components/issues",
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"repository": {
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"type": "git",
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"url": "https://github.com/GMOD/jbrowse-components.git",
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"directory": "packages/sv-core"
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},
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"author": "JBrowse Team",
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"distMain": "dist/index.js",
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"distModule": "esm/index.js",
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"srcMain": "src/index.ts",
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"srcModule": "src/index.ts",
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"main": "src/index.ts",
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"module": "",
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"files": [
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"dist",
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"esm"
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],
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"scripts": {
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"build:esm": "tsc --build tsconfig.build.esm.json",
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"build:commonjs": "tsc --build tsconfig.build.commonjs.json",
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"build": "npm run build:esm && npm run build:commonjs",
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"test": "cd ../..; jest --passWithNoTests packages/sv-core",
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"clean": "rimraf dist esm *.tsbuildinfo",
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"prebuild": "yarn clean",
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"prepack": "yarn build && yarn useDist",
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"postpack": "yarn useSrc",
40+
"useDist": "node ../../scripts/useDist.js",
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"useSrc": "node ../../scripts/useSrc.js"
42+
},
43+
"dependencies": {
44+
"@babel/runtime": "^7.16.3",
45+
"@jbrowse/app-core": "^2.15.0",
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"@jbrowse/product-core": "^2.15.0",
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"@mui/icons-material": "^6.0.0",
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"@mui/material": "^6.0.0",
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"clone": "^2.0.0",
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"copy-to-clipboard": "^3.3.1",
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"react-error-boundary": "^4.0.3"
52+
},
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"peerDependencies": {
54+
"mobx": "^6.0.0",
55+
"mobx-react": "^9.0.0",
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"mobx-state-tree": "^5.0.0",
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"react": ">=17.0.0",
58+
"react-dom": ">=17.0.0",
59+
"rxjs": "^7.0.0",
60+
"tss-react": "^4.0.0"
61+
},
62+
"publishConfig": {
63+
"access": "public"
64+
}
65+
}

‎packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx

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1+
import React, { useState } from 'react'
2+
import { observer } from 'mobx-react'
3+
import { Button, DialogActions, DialogContent } from '@mui/material'
4+
import { getSnapshot } from 'mobx-state-tree'
5+
import { Dialog } from '@jbrowse/core/ui'
6+
import { when } from 'mobx'
7+
import { getSession, Feature } from '@jbrowse/core/util'
8+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
9+
import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
10+
11+
// locals
12+
import Checkbox2 from './Checkbox2'
13+
14+
interface Display {
15+
id: string
16+
[key: string]: unknown
17+
}
18+
interface Track {
19+
id: string
20+
displays: Display[]
21+
[key: string]: unknown
22+
}
23+
24+
function stripIds(arr: Track[]) {
25+
return arr.map(({ id, displays, ...rest }) => ({
26+
...rest,
27+
displays: displays.map(({ id, ...rest }) => rest),
28+
}))
29+
}
30+
31+
const BreakendMultiLevelOptionDialog = observer(function ({
32+
model,
33+
handleClose,
34+
feature,
35+
assemblyName,
36+
viewType,
37+
view,
38+
}: {
39+
model: unknown
40+
handleClose: () => void
41+
feature: Feature
42+
view: LinearGenomeViewModel
43+
assemblyName: string
44+
viewType: {
45+
getBreakendCoveringRegions: (arg: {
46+
feature: Feature
47+
assembly: Assembly
48+
}) => {
49+
pos: number
50+
refName: string
51+
mateRefName: string
52+
matePos: number
53+
}
54+
}
55+
}) {
56+
const [copyTracks, setCopyTracks] = useState(true)
57+
const [mirror, setMirror] = useState(true)
58+
59+
return (
60+
<Dialog
61+
open
62+
onClose={handleClose}
63+
title="Multi-level breakpoint split view options"
64+
>
65+
<DialogContent>
66+
<Checkbox2
67+
checked={copyTracks}
68+
label="Copy tracks into the new view"
69+
onChange={event => {
70+
setCopyTracks(event.target.checked)
71+
}}
72+
/>
73+
74+
{copyTracks ? (
75+
<Checkbox2
76+
checked={mirror}
77+
disabled={!copyTracks}
78+
label="Mirror the copied tracks (only available if copying tracks and using two level)"
79+
onChange={event => {
80+
setMirror(event.target.checked)
81+
}}
82+
/>
83+
) : null}
84+
</DialogContent>
85+
<DialogActions>
86+
<Button
87+
onClick={() => {
88+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
89+
;(async () => {
90+
const session = getSession(model)
91+
try {
92+
const asm =
93+
await session.assemblyManager.waitForAssembly(assemblyName)
94+
if (!asm) {
95+
throw new Error(`assembly ${assemblyName} not found`)
96+
}
97+
98+
const { refName, pos, mateRefName, matePos } =
99+
viewType.getBreakendCoveringRegions({
100+
feature,
101+
assembly: asm,
102+
})
103+
104+
const viewTracks = getSnapshot(view.tracks) as Track[]
105+
const breakpointSplitView = session.addView(
106+
'BreakpointSplitView',
107+
{
108+
type: 'BreakpointSplitView',
109+
displayName: `${
110+
feature.get('name') || feature.get('id') || 'breakend'
111+
} split detail`,
112+
113+
views: [
114+
{
115+
type: 'LinearGenomeView',
116+
hideHeader: true,
117+
tracks: stripIds(getSnapshot(view.tracks)),
118+
},
119+
{
120+
type: 'LinearGenomeView',
121+
hideHeader: true,
122+
tracks: stripIds(
123+
mirror ? [...viewTracks].reverse() : viewTracks,
124+
),
125+
},
126+
],
127+
},
128+
) as unknown as { views: LinearGenomeViewModel[] }
129+
const r1 = asm.regions!.find(r => r.refName === refName)
130+
const r2 = asm.regions!.find(r => r.refName === mateRefName)
131+
if (!r1 || !r2) {
132+
throw new Error("can't find regions")
133+
}
134+
await Promise.all([
135+
breakpointSplitView.views[0]!.navToLocations([
136+
{
137+
refName,
138+
start: r1.start,
139+
end: pos,
140+
assemblyName,
141+
},
142+
{
143+
refName,
144+
start: pos + 1,
145+
end: r1.end,
146+
assemblyName,
147+
},
148+
]),
149+
breakpointSplitView.views[1]!.navToLocations([
150+
{
151+
refName: mateRefName,
152+
start: r2.start,
153+
end: matePos,
154+
assemblyName,
155+
},
156+
{
157+
refName: mateRefName,
158+
start: matePos + 1,
159+
end: r2.end,
160+
assemblyName,
161+
},
162+
]),
163+
])
164+
await when(
165+
() =>
166+
breakpointSplitView.views[1]!.initialized &&
167+
breakpointSplitView.views[0]!.initialized,
168+
)
169+
breakpointSplitView.views[1]!.zoomTo(10)
170+
breakpointSplitView.views[0]!.zoomTo(10)
171+
breakpointSplitView.views[1]!.centerAt(matePos, mateRefName)
172+
breakpointSplitView.views[0]!.centerAt(pos, refName)
173+
} catch (e) {
174+
console.error(e)
175+
session.notify(`${e}`)
176+
}
177+
})()
178+
handleClose()
179+
}}
180+
variant="contained"
181+
color="primary"
182+
autoFocus
183+
>
184+
OK
185+
</Button>
186+
<Button
187+
color="secondary"
188+
variant="contained"
189+
onClick={() => {
190+
handleClose()
191+
}}
192+
>
193+
Cancel
194+
</Button>
195+
</DialogActions>
196+
</Dialog>
197+
)
198+
})
199+
200+
export default BreakendMultiLevelOptionDialog

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