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fix: adding back default columns (#1127)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| import { | ||
| useCaseDetailsStore, | ||
| CaseVariantStatsEntry, | ||
| } from '@cases/stores/caseDetails' | ||
| import { useCaseListStore } from '@cases/stores/caseList' | ||
| import { State } from '@varfish/storeUtils' | ||
| import { computed } from 'vue' | ||
|
|
||
| export const overlayShow = computed(() => { | ||
| const caseListStore = useCaseListStore() | ||
| const caseDetailsStore = useCaseDetailsStore() | ||
| return ( | ||
| (caseListStore?.storeState?.serverInteractions ?? 0) > 0 || | ||
| (caseDetailsStore?.storeState?.serverInteractions ?? 0) > 0 | ||
| ) | ||
| }) | ||
|
|
||
| export const overlayMessage = computed(() => { | ||
| const caseListStore = useCaseListStore() | ||
| switch (caseListStore.storeState.state) { | ||
| case State.Initial: | ||
| return 'initializing...' | ||
| case State.Fetching: | ||
| return 'communication with server...' | ||
| case State.Active: | ||
| return 'all data has been loaded successfully' | ||
| case State.Error: | ||
| return 'an error occured' | ||
| default: | ||
| console.error('unknown store state', caseListStore.storeState.state) | ||
| return 'UNKNOWN STATE' | ||
| } | ||
| }) | ||
|
|
||
| export const tsTvRatio = (entry: CaseVariantStatsEntry): number => { | ||
| if (!entry.ontarget_transversions) { | ||
| return 0.0 | ||
| } else { | ||
| return entry.ontarget_transitions / entry.ontarget_transversions | ||
| } | ||
| } | ||
|
|
||
| export const downloadFile = ( | ||
| filename: string, | ||
| contents: any, | ||
| mimeType: string = 'application/octet-stream', | ||
| ) => { | ||
| const element = document.createElement('a') | ||
| element.setAttribute('href', 'data:' + mimeType + ';base64,' + btoa(contents)) | ||
| element.setAttribute('download', filename) | ||
| element.style.display = 'none' | ||
|
|
||
| document.body.appendChild(element) | ||
| element.click() | ||
| document.body.removeChild(element) | ||
| } | ||
|
|
||
| export const downloadPerSampleMetrics = (varStats: CaseVariantStatsEntry[]) => { | ||
| const result = [ | ||
| ['Sample', 'Ts', 'Tv', 'Ts/Tv', 'SNVs', 'InDels', 'MNVs', 'X hom./het.'], | ||
| ] | ||
| for (const entry of varStats) { | ||
| result.push( | ||
| [ | ||
| entry.sample_name, | ||
| entry.ontarget_transitions, | ||
| entry.ontarget_transversions, | ||
| tsTvRatio(entry), | ||
| entry.ontarget_snvs, | ||
| entry.ontarget_indels, | ||
| entry.ontarget_mnvs, | ||
| entry.chrx_het_hom, | ||
| ].map((x) => x.toString()), | ||
| ) | ||
| } | ||
| const text = result.map((row) => row.map(String).join('\t')).join('\n') | ||
| downloadFile('per-sample-metrics.tsv', text) | ||
| } | ||
|
|
||
| export interface Relatedness { | ||
| sample0: string | ||
| sample1: string | ||
| ibs0: number | ||
| ibs1: number | ||
| rel: number | ||
| } | ||
|
|
||
| export const downloadRelatedness = (relData: Relatedness[]) => { | ||
| const result = [['Sample 1', 'Sample 2', 'IBS0', 'Relatedness']] | ||
| for (const entry of relData) { | ||
| const { sample0, sample1, ibs0, rel } = entry | ||
| result.push([sample0, sample1, ibs0, rel].map((x) => x.toString())) | ||
| } | ||
| const text = result.map((row) => row.map(String).join('\t')).join('\n') | ||
| downloadFile('relatedness.tsv', text) | ||
| } |
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