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refactor(frontend): make mergeExomeAndGenome data more clear
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@rileyhgrant
rileyhgrant committed May 8, 2024
1 parent b3830a6 commit c31bc13
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Showing 3 changed files with 142 additions and 91 deletions.
98 changes: 65 additions & 33 deletions browser/src/VariantList/mergeExomeAndGenomeData.spec.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,10 @@ describe('mergeExomeAndGenomeData', () => {
ac_hom: 3,
an: 4,
af: 5,
faf95: undefined,
faf95: {
popmax: null,
popmax_population: null,
},
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects,
},
Expand All @@ -178,9 +181,8 @@ describe('mergeExomeAndGenomeData', () => {
ac_hemi: 2,
ac_hom: 3,
an: 4,
af: 5,
allele_freq: 5,
faf95: undefined,
af: 0.25,
allele_freq: 0.25,
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects,
},
Expand All @@ -201,9 +203,12 @@ describe('mergeExomeAndGenomeData', () => {
ac: 2,
ac_hemi: 3,
ac_hom: 4,
faf95: {
popmax: null,
popmax_population: null,
},
an: 5,
af: 6,
faf95: undefined,
filters: ['AC0'],
populations: genomeGeneticAncestryGroupObjects,
},
Expand All @@ -218,9 +223,8 @@ describe('mergeExomeAndGenomeData', () => {
ac_hemi: 3,
ac_hom: 4,
an: 5,
af: 6,
allele_freq: 6,
faf95: undefined,
af: 0.4,
allele_freq: 0.4,
filters: ['AC0'],
populations: genomeGeneticAncestryGroupObjects,
},
Expand Down Expand Up @@ -249,17 +253,23 @@ describe('mergeExomeAndGenomeData', () => {
ac: 1,
ac_hemi: 2,
ac_hom: 3,
faf95: {
popmax: null,
popmax_population: null,
},
an: 4,
faf95: undefined,
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects,
},
genome: {
ac: 2,
ac_hemi: 3,
ac_hom: 4,
faf95: {
popmax: null,
popmax_population: null,
},
an: 6,
faf95: undefined,
filters: ['AC0'],
populations: genomeGeneticAncestryGroupObjects,
},
Expand Down Expand Up @@ -306,19 +316,27 @@ describe('mergeExomeAndGenomeData', () => {
ac: 1,
ac_hemi: 2,
ac_hom: 3,
faf95: {
popmax: null,
popmax_population: null,
},
an: 4,
af: 5,
faf95: undefined,
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects,
},
joint: {
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
fafmax: {
faf95_max: null,
faf95_max_gen_anc: null,
faf99_max: null,
faf99_max_gen_anc: null,
},
an: 40,
faf95: undefined,
filters: ['RF'],
filters: ['discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects,
},
})
Expand All @@ -329,12 +347,12 @@ describe('mergeExomeAndGenomeData', () => {
{
...testExomeAndJointVariant,
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
ac_hemi: 20,
ac_hom: 30,
an: 40,
af: 0.25,
allele_freq: 0.25,
faf95: undefined,
filters: ['RF'],
filters: ['RF', 'discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects,
},
]
Expand All @@ -359,19 +377,27 @@ describe('mergeExomeAndGenomeData', () => {
ac: 1,
ac_hemi: 2,
ac_hom: 3,
faf95: {
popmax: null,
popmax_population: null,
},
an: 4,
af: 5,
faf95: undefined,
filters: ['RF'],
populations: genomeGeneticAncestryGroupObjects,
},
joint: {
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
fafmax: {
faf95_max: null,
faf95_max_gen_anc: null,
faf99_max: null,
faf99_max_gen_anc: null,
},
an: 40,
faf95: undefined,
filters: ['RF'],
filters: ['discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects,
},
})
Expand All @@ -382,12 +408,12 @@ describe('mergeExomeAndGenomeData', () => {
{
...testGenomeAndJointVariant,
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
ac_hemi: 20,
ac_hom: 30,
an: 40,
af: 0.25,
allele_freq: 0.25,
faf95: undefined,
filters: ['RF'],
filters: ['RF', 'discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects,
},
]
Expand Down Expand Up @@ -421,7 +447,10 @@ describe('mergeExomeAndGenomeData', () => {
ac_hom: 3,
an: 4,
af: 5,
faf95: undefined,
faf95: {
popmax: null,
popmax_population: null,
},
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects,
},
Expand All @@ -431,7 +460,10 @@ describe('mergeExomeAndGenomeData', () => {
ac_hom: 5,
an: 6,
af: 5,
faf95: undefined,
faf95: {
popmax: null,
popmax_population: null,
},
filters: ['AC0'],
populations: genomeGeneticAncestryGroupObjects,
},
Expand All @@ -440,7 +472,12 @@ describe('mergeExomeAndGenomeData', () => {
hemizygote_count: 20,
homozygote_count: 30,
an: 40,
faf95: undefined,
fafmax: {
faf95_max: null,
faf95_max_gen_anc: null,
faf99_max: null,
faf99_max_gen_anc: null,
},
filters: ['discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects,
},
Expand All @@ -458,12 +495,7 @@ describe('mergeExomeAndGenomeData', () => {
af: 0.25,
allele_freq: 0.25,
filters: ['RF', 'AC0', 'discrepant_frequencies'],
populations: [
{ ac: 9, ac_hemi: 11, ac_hom: 13, an: 90, id: 'afr' },
{ ac: 18, ac_hemi: 20, ac_hom: 22, an: 180, id: 'remaining' },
{ ac: 36, ac_hemi: 38, ac_hom: 40, an: 360, id: 'eur' },
{ ac: 64, ac_hemi: 65, ac_hom: 66, an: 640, id: 'mid' },
],
populations: jointGeneticAncestryGroupObjects,
},
]

Expand Down
123 changes: 68 additions & 55 deletions browser/src/VariantList/mergeExomeAndGenomeData.ts
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
import { Population, SequencingType } from '../VariantPage/VariantPage'
import { Filter } from '../QCFilter'
import { Population, SequencingType, Variant } from '../VariantPage/VariantPage'
import { omit } from 'lodash'

Check failure on line 3 in browser/src/VariantList/mergeExomeAndGenomeData.ts

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GitHub Actions / Checks 

'omit' is defined but never used. Allowed unused vars must match /^_/u

// safe math on possibly null values
const add = (n1: any, n2: any) => (n1 || 0) + (n2 || 0)
Expand Down Expand Up @@ -43,73 +45,84 @@ export const mergeExomeAndGenomePopulationData = (
return Object.values(populations)
}

export const mergeExomeAndGenomeData = (variants: any) =>
variants.map((variant: any) => {
type MergedVariant = Variant & {
ac: number
an: number
af: number
allele_freq: number
ac_hemi: number
ac_hom: number
filters: Filter[]
populations: Population[]
}

export const mergeExomeAndGenomeData = (variants: Variant[]): MergedVariant[] => {
const mergedVariants = variants.map((variant: Variant) => {
const { exome, genome, joint } = variant
if (!exome) {
if (!joint) {
return {
...variant,
...variant.genome,
allele_freq: variant.genome.af, // hack for variant track which expects allele_freq field
}
}

if (joint) {
const exomeFilters = exome ? exome.filters : []
const genomeFilters = genome ? genome.filters : []
const jointFilters = exomeFilters.concat(genomeFilters, joint.filters)

return {
...variant,
...variant.joint,
filters: variant.genome.filters,
allele_freq: variant.joint.ac / variant.joint.an,
ac: joint.ac,
an: joint.an,
af: joint.ac / joint.an,
allele_freq: joint.ac / joint.an,
ac_hemi: joint.hemizygote_count,
ac_hom: joint.homozygote_count,
filters: jointFilters,
populations: joint.populations,
}
}
if (!genome) {
if (!joint) {
return {
...variant,
...variant.exome,
allele_freq: variant.exome.af, // hack for variant track which expects allele_freq field
}
}
return {
...variant,
...variant.joint,
filters: variant.exome.filters,
allele_freq: variant.joint.ac / variant.joint.an, // hack for variant track which expects allele_freq field
}

const emptySequencingType = {
ac: 0,
ac_hemi: 0,
ac_hom: 0,
faf95: {
popmax: null,
popmax_population: null,
},
an: 0,
af: 5,
filters: [] as Filter[],
populations: [] as Population[],
}

const jointAC = variant.joint ? variant.joint.ac : add(exome.ac, genome.ac)
const jointAN = variant.joint ? variant.joint.an : add(exome.an, genome.an)
const jointAF = jointAC ? jointAC / jointAN : 0
const exomeOrNone = exome || emptySequencingType
const genomeOrNone = genome || emptySequencingType

const jointHemizygoteCount = variant.joint
? variant.joint.hemizygote_count
: add(exome.ac_hemi, genome.ac_hemi)
const jointHomozygoteCount = variant.joint
? variant.joint.homozygote_count
: add(exome.ac_hom, genome.ac_hom)
const combinedAC = add(exomeOrNone.ac, genomeOrNone.ac)
const combinedAN = add(exomeOrNone.an, genomeOrNone.an)
const combinedAF = combinedAC ? combinedAC / combinedAN : 0
const combinedHemizygoteCount = add(exomeOrNone.ac_hemi, genomeOrNone.ac_hemi)
const combinedHomozygoteCount = add(exomeOrNone.ac_hom, genomeOrNone.ac_hom)

const exomeAndGenomeFilters = exome.filters.concat(genome.filters)
const jointFilters = variant.joint
? exomeAndGenomeFilters.concat(variant.joint.filters)
: exomeAndGenomeFilters
const exomeFilters: Filter[] = exomeOrNone.filters
const genomeFilters: Filter[] = genomeOrNone.filters
const combinedFilters = exomeFilters.concat(genomeFilters)

const jointPopulations = variant.join
? variant.joint.populations
: mergeExomeAndGenomePopulationData(exome!, genome!)
const combinedPopulations = mergeExomeAndGenomePopulationData(
exomeOrNone as SequencingType,
genomeOrNone as SequencingType
)

const jointVariantData = {
return {
...variant,
ac: jointAC,
an: jointAN,
af: jointAF,
allele_freq: jointAF, // hack for variant track which expects allele_freq field
ac_hemi: jointHemizygoteCount,
ac_hom: jointHomozygoteCount,
filters: jointFilters,
populations: jointPopulations,
ac: combinedAC,
an: combinedAN,
af: combinedAF,
allele_freq: combinedAF,
ac_hemi: combinedHemizygoteCount,
ac_hom: combinedHomozygoteCount,
filters: combinedFilters,
populations: combinedPopulations,
}

return jointVariantData
})

return mergedVariants
}
export default mergeExomeAndGenomeData
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