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Fix ability to use LGV synteny track on inverted alignments (#3366)
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@cmdcolin
cmdcolin committed Dec 1, 2022
1 parent 1578544 commit 8435cbc
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Showing 12 changed files with 1,331 additions and 39 deletions.
74 changes: 42 additions & 32 deletions plugins/linear-comparative-view/src/LGVSyntenyDisplay/stateModelFactory.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,43 @@ import {
import { types } from 'mobx-state-tree'
import { when } from 'mobx'

// locals
import { LinearSyntenyViewModel } from '../LinearSyntenyView/model'

type LSV = LinearSyntenyViewModel

const { parseCigar } = MismatchParser

function findPosInCigar(cigar: string[], x: number) {
let featX = 0
let mateX = 0
for (let i = 0; i < cigar.length; i += 2) {
const len = +cigar[i]
const op = cigar[i + 1]
const min = Math.min(len, x - featX)

if (featX >= x) {
break
} else if (op === 'I') {
mateX += len
} else if (op === 'D') {
featX += min
} else if (op === 'M') {
mateX += min
featX += min
}
}
return [featX, mateX]
}

// eslint-disable-next-line @typescript-eslint/no-explicit-any
async function navToSynteny(feature: Feature, self: any) {
const session = getSession(self)
const track = getContainingTrack(self)
const view = getContainingView(self)
const reg = view.dynamicBlocks.contentBlocks[0]
const cigar = parseCigar(feature.get('cg') || '')
const cigar = parseCigar(feature.get('cg'))
const strand = feature.get('strand')
const regStart = reg.start
const regEnd = reg.end
const featStart = feature.get('start')
Expand All @@ -42,33 +70,15 @@ async function navToSynteny(feature: Feature, self: any) {
let rFeatEnd = featStart

if (cigar.length) {
for (let i = 0; i < cigar.length && rFeatStart < regStart; i += 2) {
const len = +cigar[i]
const op = cigar[i + 1]
if (op === 'I') {
rMateStart += len
} else if (op === 'D') {
rFeatStart += len
} else if (op === 'M') {
const l2 = Math.min(len, regStart - rFeatStart)
const [featStartX, mateStartX] = findPosInCigar(cigar, regStart - featStart)
const [featEndX, mateEndX] = findPosInCigar(cigar, regEnd - featStart)

rMateStart += l2
rFeatStart += l2
}
}
for (let i = 0; i < cigar.length && rFeatEnd < regEnd; i += 2) {
const len = +cigar[i]
const op = cigar[i + 1]
if (op === 'I') {
rMateEnd += len
} else if (op === 'D') {
rFeatEnd += len
} else if (op === 'M') {
const l2 = Math.min(len, regEnd - rFeatEnd)
rMateEnd += l2
rFeatEnd += l2
}
}
// avoid multiply by 0 with strand undefined
const flipper = strand === -1 ? -1 : 1
rFeatStart = featStart + featStartX
rFeatEnd = featStart + featEndX
rMateStart = mateStart + mateStartX * flipper
rMateEnd = mateStart + mateEndX * flipper
} else {
rFeatEnd = featEnd
rMateEnd = mateEnd
Expand Down Expand Up @@ -101,20 +111,20 @@ async function navToSynteny(feature: Feature, self: any) {
],
},
],
})
}) as LSV
const f = (n: number) => Math.floor(n)
const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`
const l2 = `${mateRef}:${f(rMateStart)}-${f(rMateEnd)}`
const l2 = `${mateRef}:${f(rMateStart)}-${f(rMateEnd)}${
strand === -1 ? '[rev]' : ''
}`
await when(() => view2.width !== undefined)
// @ts-ignore
view2.views[0].navToLocString(l1, featAsm)
// @ts-ignore
view2.views[1].navToLocString(l2, mateAsm)
}

/**
* #stateModel LGVSyntenyDisplay
* extends `LinearBasicDisplay`, displays location of "synteny" feature in a
* extends `LinearPileupDisplay`, displays location of "synteny" feature in a
* plain LGV, allowing linking out to external synteny views
*/
function stateModelFactory(schema: AnyConfigurationSchemaType) {
Expand Down
2 changes: 1 addition & 1 deletion products/jbrowse-img/test/svg_from_volvox_fasta_and_bam_norasterize.svg
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120 changes: 120 additions & 0 deletions products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -289,6 +289,44 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"type": "ReferenceSequenceTrack",
},
},
{
"name": "volvox-rev-del",
"sequence": {
"adapter": {
"faiLocation": {
"internetAccountId": undefined,
"internetAccountPreAuthorization": undefined,
"locationType": "UriLocation",
"uri": "volvox-rev-del.fa.fai",
},
"fastaLocation": {
"internetAccountId": undefined,
"internetAccountPreAuthorization": undefined,
"locationType": "UriLocation",
"uri": "volvox-rev-del.fa",
},
"metadataLocation": {
"internetAccountId": undefined,
"internetAccountPreAuthorization": undefined,
"locationType": "UriLocation",
"uri": "/path/to/fa.metadata.yaml",
},
"type": "IndexedFastaAdapter",
},
"displays": [
{
"displayId": "volvox-rev-del-ReferenceSequenceTrack-LinearReferenceSequenceDisplay",
"type": "LinearReferenceSequenceDisplay",
},
{
"displayId": "volvox-rev-del-ReferenceSequenceTrack-LinearGCContentDisplay",
"type": "LinearGCContentDisplay",
},
],
"trackId": "volvox-rev-del-ReferenceSequenceTrack",
"type": "ReferenceSequenceTrack",
},
},
],
"configuration": {},
"connections": [],
Expand Down Expand Up @@ -2424,6 +2462,9 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"volvox",
"volvox",
],
"category": [
"Synteny",
],
"displays": [
{
"displayId": "volvox_fake_synteny_alt-DotplotDisplay",
Expand Down Expand Up @@ -2464,6 +2505,9 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"volvox",
"volvox",
],
"category": [
"Synteny",
],
"displays": [
{
"displayId": "volvox_fake_synteny-DotplotDisplay",
Expand Down Expand Up @@ -3173,6 +3217,9 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"volvox",
"volvox_del",
],
"category": [
"Synteny",
],
"displays": [
{
"displayId": "volvox_del.paf-1658813720770-DotplotDisplay",
Expand Down Expand Up @@ -3211,6 +3258,9 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"volvox",
"volvox_ins",
],
"category": [
"Synteny",
],
"displays": [
{
"displayId": "volvox_ins.paf-1658813720770-DotplotDisplay",
Expand Down Expand Up @@ -3293,6 +3343,76 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
"trackId": "variant_effect_demo_jannovar",
"type": "VariantTrack",
},
{
"adapter": {
"assemblyNames": [
"volvox-rev-del",
"volvox",
],
"pafLocation": {
"internetAccountId": undefined,
"internetAccountPreAuthorization": undefined,
"locationType": "UriLocation",
"uri": "volvox-rev-del.paf",
},
"type": "PAFAdapter",
},
"assemblyNames": [
"volvox-rev-del",
"volvox",
],
"category": [
"Synteny",
],
"displays": [
{
"displayId": "volvox-rev-del-DotplotDisplay",
"type": "DotplotDisplay",
},
{
"displayId": "volvox-rev-del-LinearComparativeDisplay",
"type": "LinearComparativeDisplay",
},
{
"displayId": "volvox-rev-del-LinearSyntenyDisplay",
"type": "LinearSyntenyDisplay",
},
{
"displayId": "volvox-rev-del-LGVSyntenyDisplay",
"type": "LGVSyntenyDisplay",
},
],
"name": "volvox-rev-del",
"trackId": "volvox-rev-del",
"type": "SyntenyTrack",
},
{
"adapter": {
"gffLocation": {
"internetAccountId": undefined,
"internetAccountPreAuthorization": undefined,
"locationType": "UriLocation",
"uri": "volvox-rev-del.gff",
},
"type": "Gff3Adapter",
},
"assemblyNames": [
"volvox-rev-del",
],
"displays": [
{
"displayId": "volvox-rev-del-annotations-LinearBasicDisplay",
"type": "LinearBasicDisplay",
},
{
"displayId": "volvox-rev-del-annotations-LinearArcDisplay",
"type": "LinearArcDisplay",
},
],
"name": "volvox-rev-del-annotations",
"trackId": "volvox-rev-del-annotations",
"type": "FeatureTrack",
},
],
}
`;
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