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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| import { API_BASE_PREFIX_NGINX } from '@/api/common' | ||
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| const API_BASE_URL = `${API_BASE_PREFIX_NGINX}/` | ||
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| const visibilityWindow = 10000000 | ||
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| const hescTadTrack = { | ||
| name: 'hESC TADs', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/hesc.bed`, | ||
| color: 'gray' | ||
| } | ||
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| const curatedMmsTrack = { | ||
| name: 'Curated MMS', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/patho-mms.bed`, | ||
| color: 'red' | ||
| } | ||
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| // const clinvarTrack = { | ||
| // name: 'ClinVar SVs', | ||
| // sourceType: 'custom', | ||
| // visibilityWindow, | ||
| // height: 100, | ||
| // displayMode: 'SQUISHED', | ||
| // source: { | ||
| // url: `/svs/worker/clinvar/grch37/?min_pathogenicity=likely-pathogenic&chromosome=$CHR&begin=$START&end=$END`, | ||
| // method: 'GET', | ||
| // contentType: 'application/json', | ||
| // mappings: { | ||
| // chr: 'chromosome', | ||
| // start: 'begin', | ||
| // }, | ||
| // queryable: true, | ||
| // }, | ||
| // format: 'annotation', | ||
| // colorBy: 'pathogenicity', | ||
| // colorTable: { | ||
| // pathogenic: 'red', | ||
| // 'likely-pathogenic': 'orange', | ||
| // uncertain: 'blue', | ||
| // 'likely-benign': 'gray', | ||
| // benign: 'light gray', | ||
| // }, | ||
| // } | ||
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| const duplicationTrack = { | ||
| name: 'UCSC Segmental Duplications', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/genomicSuperDups.bed.gz`, | ||
| indexURL: `${API_BASE_URL}grch37/genomicSuperDups.bed.gz.tbi`, | ||
| color: 'black' | ||
| } | ||
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| const repeatsTrack = { | ||
| name: 'UCSC Repeat Masker', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/rmsk.bed.gz`, | ||
| indexURL: `${API_BASE_URL}grch37/rmsk.bed.gz.tbi`, | ||
| color: 'black' | ||
| } | ||
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| const altTrack = { | ||
| name: 'UCSC Alt Loci Track', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/altSeqLiftOverPsl.bed.gz`, | ||
| indexURL: `${API_BASE_URL}grch37/altSeqLiftOverPsl.bed.gz.tbi`, | ||
| color: 'black' | ||
| } | ||
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| const fixTrack = { | ||
| name: 'UCSC Fix Track', | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| url: `${API_BASE_URL}grch37/fixSeqLiftOverPsl.bed.gz`, | ||
| indexURL: `${API_BASE_URL}grch37/fixSeqLiftOverPsl.bed.gz.tbi`, | ||
| color: 'black' | ||
| } | ||
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| const bgDbTracks = [ | ||
| // { | ||
| // title: 'In-House SVs', | ||
| // token: 'inhouse', | ||
| // }, | ||
| { | ||
| title: 'gnomad-SV', | ||
| token: 'gnomad' | ||
| }, | ||
| { | ||
| title: 'DGV SVs', | ||
| token: 'dgv' | ||
| }, | ||
| { | ||
| title: 'DGV GS SVs', | ||
| token: 'dgv-gs' | ||
| }, | ||
| { | ||
| title: 'ExAC CNVs', | ||
| token: 'exac' | ||
| } | ||
| ].map(({ title, token }) => { | ||
| return { | ||
| name: title, | ||
| sourceType: 'annotation', | ||
| format: 'bed', | ||
| visibilityWindow, | ||
| displayMode: 'SQUISHED', | ||
| url: `${API_BASE_URL}grch37/${token}.bed.gz`, | ||
| indexURL: `${API_BASE_URL}grch37/${token}.bed.gz.tbi`, | ||
| color: 'black' | ||
| } | ||
| }) | ||
| export const publicTracks = [ | ||
| duplicationTrack, | ||
| repeatsTrack, | ||
| altTrack, | ||
| fixTrack, | ||
| hescTadTrack, | ||
| curatedMmsTrack | ||
| // clinvarTrack, | ||
| ].concat(bgDbTracks) | ||
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| export const genCaseTrack = (caseUuid: string) => ({ | ||
| order: -1, | ||
| height: '200', | ||
| name: 'Case SVs', | ||
| sourceType: 'custom', | ||
| visibilityWindow, | ||
| source: { | ||
| url: `/svs/ajax/fetch-variants/${caseUuid}/?chromosome=$CHR&start=$START&end=$END`, | ||
| // url: `https://varfish.bihealth.org/svs/ajax/fetch-variants/7a538a72-f8fb-4d71-a08b-6045f1e983dc/?chromosome=chr15&start=16989370.8&end=26828561.7`, | ||
| method: 'GET', | ||
| contentType: 'application/json', | ||
| mappings: { | ||
| chr: 'chromosome' | ||
| }, | ||
| queryable: true | ||
| }, | ||
| format: 'annotation', | ||
| colorBy: 'sv_type', | ||
| colorTable: { | ||
| DEL: 'red', | ||
| DUP: 'green', | ||
| INV: 'blue', | ||
| '*': 'black' | ||
| } | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| <script setup lang="ts"> | ||
| import { ref, onMounted, watch } from 'vue' | ||
| import igv from 'igv' | ||
| // import { genCaseTrack, publicTracks } from '@/components/GenomeBrowser.tracks' | ||
| /** Alias for Genome Browser type. */ | ||
| type GenomeBrowser = any | ||
| // Define the props. | ||
| const props = defineProps({ | ||
| // Case UUID | ||
| caseUuid: String, | ||
| // Genome build, e.g., "hg19" or "b37" | ||
| genome: String, | ||
| // Locus to go to, e.g., "chr1:1,900,000-2,000,000" | ||
| locus: String | ||
| }) | ||
| // The <div> to show the browser in. | ||
| const genomeBrowserDivRef = ref(null) | ||
| // Set on IGV browser creation. | ||
| const igvBrowser = ref(null) | ||
| const translateGenome = (value: any) => { | ||
| if (value === 'GRCh37') { | ||
| return 'hg19' | ||
| } else if (value === 'GRCh38') { | ||
| return 'b38' | ||
| } else { | ||
| return value | ||
| } | ||
| } | ||
| // Conditionally add case tracks. | ||
| // const addCaseTracks = (browser: GenomeBrowser) => { | ||
| // if (props.caseUuid) { | ||
| // console.log(genCaseTrack(props.caseUuid)) | ||
| // browser.loadTrack(genCaseTrack(props.caseUuid)) | ||
| // } | ||
| // } | ||
| // Add all tracks. | ||
| // const addTracks = (browser: any) => { | ||
| // addCaseTracks(browser) | ||
| // for (const track of publicTracks) { | ||
| // browser.loadTrack(track) | ||
| // } | ||
| // } | ||
| // Watch changes to the genome (requires full reload). | ||
| watch( | ||
| () => props.genome, | ||
| () => { | ||
| igvBrowser.value?.loadGenome(translateGenome(props.genome)).then((browser: GenomeBrowser) => { | ||
| browser.search(props.locus) | ||
| }) | ||
| // .then((browser: GenomeBrowser) => { | ||
| // addTracks(browser) | ||
| // }) | ||
| } | ||
| ) | ||
| // Watch changes to the case (requires track reload). | ||
| watch( | ||
| () => props.caseUuid, | ||
| () => { | ||
| if (igvBrowser.value) { | ||
| igvBrowser.value.removeTrackByName('Case SVs') | ||
| // addCaseTracks(igvBrowser.value) | ||
| } | ||
| } | ||
| ) | ||
| // Watch changes to the locus (jumping is enough). | ||
| watch( | ||
| () => props.locus, | ||
| () => { | ||
| if (igvBrowser.value) { | ||
| igvBrowser.value.search(props.locus) | ||
| } | ||
| } | ||
| ) | ||
| // Construct igv.js browser when mounted. | ||
| onMounted(() => { | ||
| igv | ||
| .createBrowser(genomeBrowserDivRef.value, { | ||
| genome: translateGenome(props.genome), | ||
| locus: props.locus | ||
| }) | ||
| .then((browser: GenomeBrowser) => { | ||
| igvBrowser.value = browser | ||
| // addTracks(browser) | ||
| if (props.locus) { | ||
| igvBrowser.value?.search(props.locus) | ||
| } | ||
| }) | ||
| }) | ||
| </script> | ||
|
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| <template> | ||
| <div ref="genomeBrowserDivRef"></div> | ||
| </template> |
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