@molgenis/vip-report-template 2.7.3 → 3.0.0-beta
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.eslintignore +4 -0
- package/.eslintrc.js +16 -22
- package/.gitattributes +1 -0
- package/.husky/pre-commit +4 -0
- package/.prettierignore +4 -0
- package/.prettierrc.json +3 -0
- package/.travis.yml +14 -11
- package/README.md +7 -29
- package/index.html +12 -0
- package/package.json +42 -55
- package/src/Api.ts +12 -0
- package/src/App.tsx +101 -0
- package/src/__tests__/decisionTreeUtils.test.ts +75 -0
- package/src/__tests__/field.test.ts +107 -0
- package/src/__tests__/query.test.ts +99 -0
- package/src/__tests__/sortUtils.test.ts +83 -0
- package/src/__tests__/utils.test.ts +24 -0
- package/src/__tests__/viewUtils.test.ts +125 -0
- package/src/assets/sass/main.scss +113 -0
- package/src/components/Abbr.tsx +20 -0
- package/src/components/Anchor.tsx +12 -0
- package/src/components/Breadcrumb.tsx +33 -0
- package/src/components/Checkbox.tsx +32 -0
- package/src/components/ConsequenceTable.tsx +38 -0
- package/src/components/DatasetDropdown.tsx +44 -0
- package/src/components/Error.tsx +9 -0
- package/src/components/FieldHeader.tsx +26 -0
- package/src/components/GenomeBrowser.tsx +114 -0
- package/src/components/InfoCollapsablePane.tsx +68 -0
- package/src/components/Loader.tsx +5 -0
- package/src/components/SampleTable.tsx +118 -0
- package/src/components/SearchBox.tsx +44 -0
- package/src/components/Sort.tsx +58 -0
- package/src/components/VariantInfoNestedTable.tsx +117 -0
- package/src/components/VariantInfoTable.tsx +30 -0
- package/src/components/VariantSampleTable.tsx +56 -0
- package/src/components/VariantTable.tsx +71 -0
- package/src/components/VariantsSampleTable.tsx +87 -0
- package/src/components/VariantsTable.tsx +135 -0
- package/src/components/VcfHeaderRow.tsx +15 -0
- package/src/components/filter/Filter.tsx +34 -0
- package/src/components/filter/FilterCategorical.tsx +66 -0
- package/src/components/filter/FilterIntegerDp.tsx +24 -0
- package/src/components/filter/FilterIntegerVid.tsx +28 -0
- package/src/components/filter/FilterIntegerVim.tsx +24 -0
- package/src/components/filter/Filters.tsx +27 -0
- package/src/components/filter/InfoFilter.tsx +36 -0
- package/src/components/filter/InfoFilters.tsx +32 -0
- package/src/components/filter/SampleFilters.tsx +44 -0
- package/src/components/filter/SamplesFilters.tsx +31 -0
- package/src/components/record/Allele.tsx +38 -0
- package/src/components/record/AlleleBreakend.tsx +5 -0
- package/src/components/record/AlleleMissing.tsx +5 -0
- package/src/components/record/AlleleNucs.tsx +49 -0
- package/src/components/record/AlleleSymbolic.tsx +5 -0
- package/src/components/record/Alt.tsx +17 -0
- package/src/components/record/Chrom.tsx +5 -0
- package/src/components/record/Filter.tsx +9 -0
- package/src/components/record/Format.tsx +31 -0
- package/src/components/record/Id.tsx +9 -0
- package/src/components/record/Info.tsx +53 -0
- package/src/components/record/Pager.tsx +64 -0
- package/src/components/record/Pos.tsx +5 -0
- package/src/components/record/Qual.tsx +5 -0
- package/src/components/record/RecordDownload.tsx +36 -0
- package/src/components/record/Ref.tsx +6 -0
- package/src/components/record/field/Field.tsx +20 -0
- package/src/components/record/field/FieldMultipleValue.tsx +22 -0
- package/src/components/record/field/FieldSingleValue.tsx +35 -0
- package/src/components/record/field/FieldValueCharacter.tsx +11 -0
- package/src/components/record/field/FieldValueFlag.tsx +11 -0
- package/src/components/record/field/FieldValueFloat.tsx +17 -0
- package/src/components/record/field/FieldValueInteger.tsx +11 -0
- package/src/components/record/field/FieldValueString.tsx +14 -0
- package/src/components/record/format/GenotypeField.tsx +63 -0
- package/src/components/record/info/ClinVar.tsx +37 -0
- package/src/components/record/info/Consequence.tsx +19 -0
- package/src/components/record/info/Gene.tsx +11 -0
- package/src/components/record/info/GnomAD.tsx +29 -0
- package/src/components/record/info/Hgvs.tsx +18 -0
- package/src/components/record/info/HpoTerm.tsx +12 -0
- package/src/components/record/info/PubMed.tsx +19 -0
- package/src/components/tree/DecisionTreeBoolMultiQuery.tsx +21 -0
- package/src/components/tree/DecisionTreeBoolQuery.tsx +22 -0
- package/src/components/tree/DecisionTreeNode.tsx +64 -0
- package/src/components/tree/DecisionTreeNodeBool.tsx +35 -0
- package/src/components/tree/DecisionTreeNodeBoolMulti.tsx +32 -0
- package/src/components/tree/DecisionTreeNodeCategorical.tsx +32 -0
- package/src/components/tree/DecisionTreeNodeExists.tsx +25 -0
- package/src/components/tree/DecisionTreeNodeLeaf.tsx +6 -0
- package/src/components/tree/DecisionTreeOutcomeNode.tsx +11 -0
- package/src/components/tree/DecisionTreePath.tsx +27 -0
- package/src/igv.d.ts +4 -1
- package/src/index.tsx +40 -0
- package/src/mocks/GRCh37/alignment.bam.blob +0 -0
- package/src/mocks/GRCh37/decisionTree.json +354 -0
- package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-152520538-152521038.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-16375333-16375833.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-16376162-16376662.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17348965-17349469.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17348969-17349469.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17354844-17355344.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/10-126091249-126091749.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/11-134013975-134014475.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/13-77569878-77570378.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-105167610-105168110.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89307588-89308088.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89309945-89310445.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89336157-89336657.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29555814-29556314.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29585172-29585672.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29663629-29664129.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29675976-29676476.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29683733-29684233.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-11215896-11216396.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-11223801-11224301.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-17449149-17449649.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-17451747-17452247.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/2-47635417-47635917.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/20-62326742-62327242.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/22-50627343-50627843.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/22-50721296-50721796.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/4-106320044-106320544.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/7-42017061-42017561.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/7-42064707-42065207.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/8-145140250-145140750.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/8-61764893-61765393.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/9-107546383-107546883.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/9-107584614-107585114.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/MT-15076-15576.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/X-48932771-48933271.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/genes.txt.gz.blob +0 -0
- package/src/mocks/GRCh37/static.ts +192 -0
- package/src/mocks/GRCh37/vcf/family.vcf.blob +104 -0
- package/src/mocks/GRCh37/vcf/no_vep.vcf.blob +61 -0
- package/src/mocks/GRCh37/vcf/samples_0.vcf.blob +93 -0
- package/src/mocks/GRCh37/vcf/samples_1.vcf.blob +93 -0
- package/src/mocks/GRCh37/vcf/samples_100.vcf.blob +93 -0
- package/src/mocks/GRCh38/alignment.bam.blob +0 -0
- package/src/mocks/GRCh38/decisionTree.json +369 -0
- package/src/mocks/GRCh38/fasta/chr1-152548062-152548562.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr1-16049667-16050167.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr1-17022474-17022974.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr1-9982230-9982730.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr10-124402680-124403180.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr11-134144080-134144580.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr13-76995743-76996243.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr14-104701273-104701773.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr14-88869813-88870313.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr17-31228796-31229296.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr17-31336611-31337111.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr19-11105220-11105720.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr19-17340938-17341438.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr2-47408278-47408778.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr20-63695389-63695889.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr22-50188914-50189414.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr22-50282867-50283367.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr4-105398887-105399387.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr7-41977462-41977962.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr7-42025108-42025608.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr8-144085347-144085847.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr8-60852334-60852834.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chr9-104784102-104784602.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chrM-15075-15575.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chrX-49075112-49075612.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/fasta/chrY-2787350-2787850.fasta.gz.blob +0 -0
- package/src/mocks/GRCh38/genes.txt.gz.blob +0 -0
- package/src/mocks/GRCh38/static.ts +170 -0
- package/src/mocks/GRCh38/vcf/family.vcf.blob +270 -0
- package/src/mocks/GRCh38/vcf/no_vep.vcf.blob +238 -0
- package/src/mocks/GRCh38/vcf/samples_0.vcf.blob +265 -0
- package/src/mocks/GRCh38/vcf/samples_1.vcf.blob +266 -0
- package/src/mocks/GRCh38/vcf/samples_100.vcf.blob +266 -0
- package/src/mocks/MockApiClient.ts +375 -0
- package/src/mocks/static.ts +1636 -0
- package/src/mocks/utils.ts +16 -0
- package/src/store/index.tsx +163 -0
- package/src/utils/ApiUtils.ts +253 -0
- package/src/utils/decisionTreeUtils.ts +14 -0
- package/src/utils/field.ts +49 -0
- package/src/utils/query.ts +130 -0
- package/src/utils/sample.ts +5 -0
- package/src/utils/sortUtils.ts +65 -0
- package/src/utils/utils.ts +3 -0
- package/src/utils/viewUtils.ts +38 -0
- package/src/views/Home.tsx +121 -0
- package/src/views/Sample.tsx +26 -0
- package/src/views/SampleVariant.tsx +115 -0
- package/src/views/SampleVariantConsequence.tsx +105 -0
- package/src/views/SampleVariants.tsx +244 -0
- package/src/views/Samples.tsx +57 -0
- package/src/views/Variant.tsx +63 -0
- package/src/views/VariantConsequence.tsx +69 -0
- package/src/views/Variants.tsx +123 -0
- package/src/views/data/SampleData.tsx +11 -0
- package/src/views/data/SampleVariantConsequenceData.tsx +12 -0
- package/src/views/data/SampleVariantData.tsx +13 -0
- package/src/views/data/VariantConsequenceData.tsx +9 -0
- package/src/views/data/VariantData.tsx +12 -0
- package/tsconfig.json +9 -39
- package/vite.config.ts +18 -0
- package/.browserslistrc +0 -3
- package/.env +0 -2
- package/.prettierrc +0 -5
- package/.scannerwork/.sonar_lock +0 -0
- package/.scannerwork/css-bundle/stylelintconfig.json +0 -1
- package/.scannerwork/report-task.txt +0 -8
- package/.scannerwork/ucfg2/js/_home_travis_build_molgenis_vip_report_template_src_App_vue_1_1_P1_ENTRY.ucfg +0 -0
- package/.scannerwork/ucfg2/js/_home_travis_build_molgenis_vip_report_template_src_components_Alerts_vue_1_1_P1_ENTRY.ucfg +0 -0
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:readDepth="data.item.s[sample.index].DP"
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53
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:allelicDepth="data.item.s[sample.index].AD"
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54
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/>
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55
|
-
</template>
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56
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<template v-slot:cell(father)="data">
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57
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<Genotype
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58
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:genotype="data.item.s[samplePaternal.index].GT"
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59
|
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:alleles="[data.item.r].concat(data.item.a)"
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60
|
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:readDepth="data.item.s[samplePaternal.index].DP"
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61
|
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:allelicDepth="data.item.s[samplePaternal.index].AD"
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62
|
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/>
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63
|
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</template>
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64
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<template v-slot:cell(mother)="data">
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65
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<Genotype
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66
|
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:genotype="data.item.s[sampleMaternal.index].GT"
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67
|
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:alleles="[data.item.r].concat(data.item.a)"
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68
|
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:readDepth="data.item.s[sampleMaternal.index].DP"
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69
|
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:allelicDepth="data.item.s[sampleMaternal.index].AD"
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70
|
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/>
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71
|
-
</template>
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72
|
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<template v-slot:cell(expand)="data">
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73
|
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<b-button
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74
|
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v-if="data.item.effect.items.length > 1"
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75
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class="btn-xs"
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76
|
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@click="data.item.expand = !data.item.expand"
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77
|
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mr="3"
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78
|
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>
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79
|
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<b-icon-chevron-up v-if="data.item.expand" />
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80
|
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<b-icon-chevron-down v-else />
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81
|
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</b-button>
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82
|
-
</template>
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83
|
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<template v-slot:cell(effect)="data">
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84
|
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<RecordInfoDetailsItemMultiline
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|
85
|
-
:metadata="data.item.effect.metadata"
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86
|
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:values="data.item.expand ? data.item.effect.items : data.item.effect.items.slice(0, 1)"
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87
|
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/>
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88
|
-
</template>
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89
|
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<template v-slot:cell(gene)="data">
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90
|
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<RecordInfoDetailsItemMultiline
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91
|
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:metadata="data.item.gene.metadata"
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92
|
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:values="data.item.expand ? data.item.gene.items : data.item.gene.items.slice(0, 1)"
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93
|
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/>
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94
|
-
</template>
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95
|
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<template v-slot:cell(inheritance)="data">
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96
|
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<RecordInfoDetailsItemMultiline
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|
97
|
-
:metadata="data.item.inheritance.metadata"
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98
|
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:values="data.item.expand ? data.item.inheritance.items : data.item.inheritance.items.slice(0, 1)"
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99
|
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/>
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100
|
-
</template>
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101
|
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<template v-slot:cell(hgvsC)="data">
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102
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<RecordInfoDetailsItemMultiline
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103
|
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:metadata="data.item.hgvsC.metadata"
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104
|
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:values="data.item.expand ? data.item.hgvsC.items : data.item.hgvsC.items.slice(0, 1)"
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105
|
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/>
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106
|
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</template>
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107
|
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<template v-slot:cell(hgvsP)="data">
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108
|
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<RecordInfoDetailsItemMultiline
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109
|
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:metadata="data.item.hgvsP.metadata"
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110
|
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:values="data.item.expand ? data.item.hgvsP.items : data.item.hgvsP.items.slice(0, 1)"
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111
|
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/>
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112
|
-
</template>
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113
|
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<template v-slot:cell(gnomAD)="data">
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114
|
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<RecordInfoDetailsItemMultiline
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115
|
-
:metadata="data.item.gnomAD.metadata"
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116
|
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:values="data.item.expand ? data.item.gnomAD.items : data.item.gnomAD.items.slice(0, 1)"
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117
|
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/>
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118
|
-
</template>
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119
|
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<template v-slot:cell(mvl)="data">
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120
|
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<RecordInfoDetailsItemMultiline
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121
|
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:metadata="data.item.mvl.metadata"
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122
|
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:values="data.item.expand ? data.item.mvl.items : data.item.mvl.items.slice(0, 1)"
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123
|
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/>
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124
|
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</template>
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125
|
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<template v-slot:cell(vkgl)="data">
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126
|
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<RecordInfoDetailsItemMultiline
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127
|
-
:metadata="data.item.vkgl.metadata"
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128
|
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:values="data.item.expand ? data.item.vkgl.items : data.item.vkgl.items.slice(0, 1)"
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129
|
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/>
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130
|
-
</template>
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131
|
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<template v-slot:cell(clinVar)="data">
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132
|
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<RecordInfoDetailsItemMultiline
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133
|
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:metadata="data.item.clinVar.metadata"
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134
|
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:values="data.item.expand ? data.item.clinVar.items : data.item.clinVar.items.slice(0, 1)"
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135
|
-
/>
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136
|
-
</template>
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137
|
-
<template v-slot:cell(pubMed)="data">
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|
138
|
-
<RecordInfoDetailsItemMultiline
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|
139
|
-
:metadata="data.item.pubMed.metadata"
|
|
140
|
-
:values="data.item.expand ? data.item.pubMed.items : data.item.pubMed.items.slice(0, 1)"
|
|
141
|
-
/>
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|
142
|
-
</template>
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|
143
|
-
<template v-slot:cell(capice)="data">
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|
144
|
-
<span v-if="data.item.n !== undefined && data.item.n['CAP'] !== undefined">
|
|
145
|
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<span v-for="(score, index) in data.item.n['CAP']" :key="index">
|
|
146
|
-
<span>{{ score.toFixed(4) }}</span>
|
|
147
|
-
<span v-if="index < data.item.n['CAP'].length - 1">, </span>
|
|
148
|
-
</span>
|
|
149
|
-
</span>
|
|
150
|
-
</template>
|
|
151
|
-
<template v-slot:cell(geneMatch)="data">
|
|
152
|
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<AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="geneMatch" />
|
|
153
|
-
</template>
|
|
154
|
-
<template v-slot:cell(class)="data">
|
|
155
|
-
<AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="class" />
|
|
156
|
-
</template>
|
|
157
|
-
<template v-slot:cell(txt)="data">
|
|
158
|
-
<AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="notes" />
|
|
159
|
-
</template>
|
|
160
|
-
</b-table>
|
|
161
|
-
<b-row>
|
|
162
|
-
<b-col offset="3" cols="6">
|
|
163
|
-
<b-pagination
|
|
164
|
-
v-if="page.totalPages > 1"
|
|
165
|
-
v-model="page.currentPage"
|
|
166
|
-
:total-rows="page.totalRows"
|
|
167
|
-
:per-page="page.perPage"
|
|
168
|
-
align="center"
|
|
169
|
-
aria-controls="classifier-table"
|
|
170
|
-
></b-pagination>
|
|
171
|
-
</b-col>
|
|
172
|
-
<b-col cols="3" class="text-right">
|
|
173
|
-
<span v-if="page.totalRows > 0"
|
|
174
|
-
><em>{{ page.totalRows }} {{ $t(page.totalRows === 1 ? 'record' : 'records') }}</em></span
|
|
175
|
-
>
|
|
176
|
-
</b-col>
|
|
177
|
-
</b-row>
|
|
178
|
-
<b-modal :id="infoModal.id" size="xl" :title="$t('recordDetails')" no-fade ok-only @hide="resetInfoModal">
|
|
179
|
-
<template v-slot:modal-ok>
|
|
180
|
-
{{ $t('ok') }}
|
|
181
|
-
</template>
|
|
182
|
-
<div class="modal-container">
|
|
183
|
-
<RecordDetails
|
|
184
|
-
v-if="infoModal.record"
|
|
185
|
-
:metadata="metadata.records"
|
|
186
|
-
:record="infoModal.record"
|
|
187
|
-
:sample="sample"
|
|
188
|
-
/>
|
|
189
|
-
</div>
|
|
190
|
-
</b-modal>
|
|
191
|
-
</div>
|
|
192
|
-
</template>
|
|
193
|
-
|
|
194
|
-
<script lang="ts">
|
|
195
|
-
import { mapActions, mapGetters, mapState } from 'vuex';
|
|
196
|
-
import Vue, { PropType } from 'vue';
|
|
197
|
-
import { BButton, BTable, BvTableCtxObject, BvTableFieldArray } from 'bootstrap-vue';
|
|
198
|
-
import { Api, Vcf } from '@molgenis/vip-report-api';
|
|
199
|
-
import { append, formatNumber } from '@/globals/filters';
|
|
200
|
-
import RecordDetails from '@/components/RecordDetails.vue';
|
|
201
|
-
import Allele from '@/components/Allele.vue';
|
|
202
|
-
import Genotype from '@/components/Genotype.vue';
|
|
203
|
-
import { getConsequences, getVariant, getInheritanceModesGeneSelector, getPhenotypesSelector } from '@/globals/utils';
|
|
204
|
-
import { Consequences } from '@/types/Consequence';
|
|
205
|
-
import RecordInfoDetailsItemMultiline from '@/components/RecordInfoDetailsItemMultiline.vue';
|
|
206
|
-
import { Annotation } from '@/types/Annotations';
|
|
207
|
-
import AnnotationControl from '@/components/annotation/AnnotationControl.vue';
|
|
208
|
-
import RecordTableControls from '@/components/RecordTableControls.vue';
|
|
209
|
-
|
|
210
|
-
interface Page {
|
|
211
|
-
currentPage: number;
|
|
212
|
-
perPage: number;
|
|
213
|
-
totalRows: number;
|
|
214
|
-
totalPages: number;
|
|
215
|
-
}
|
|
216
|
-
|
|
217
|
-
interface InfoModal {
|
|
218
|
-
id: string;
|
|
219
|
-
title: string;
|
|
220
|
-
record: Vcf.Record | null;
|
|
221
|
-
}
|
|
222
|
-
|
|
223
|
-
interface Row {
|
|
224
|
-
c: string;
|
|
225
|
-
p: number;
|
|
226
|
-
r: string;
|
|
227
|
-
a: (string | null)[];
|
|
228
|
-
q: number | null;
|
|
229
|
-
f: string[];
|
|
230
|
-
s: Vcf.RecordSample[];
|
|
231
|
-
effect?: unknown;
|
|
232
|
-
gene?: unknown;
|
|
233
|
-
inheritance?: unknown;
|
|
234
|
-
hgvsC?: unknown;
|
|
235
|
-
hgvsP?: unknown;
|
|
236
|
-
pubMed?: unknown;
|
|
237
|
-
clinVar?: unknown;
|
|
238
|
-
gnomAD?: unknown;
|
|
239
|
-
mvl?: unknown;
|
|
240
|
-
vkgl?: unknown;
|
|
241
|
-
expand?: boolean;
|
|
242
|
-
annotation?: Annotation;
|
|
243
|
-
}
|
|
244
|
-
|
|
245
|
-
export default Vue.extend({
|
|
246
|
-
components: {
|
|
247
|
-
Allele,
|
|
248
|
-
AnnotationControl,
|
|
249
|
-
Genotype,
|
|
250
|
-
RecordDetails,
|
|
251
|
-
RecordInfoDetailsItemMultiline,
|
|
252
|
-
RecordTableControls
|
|
253
|
-
},
|
|
254
|
-
props: {
|
|
255
|
-
sample: { type: Object as PropType<Api.Sample>, required: false }
|
|
256
|
-
},
|
|
257
|
-
data: function () {
|
|
258
|
-
return {
|
|
259
|
-
isTableBusy: false as boolean,
|
|
260
|
-
sortBy: null as string | null,
|
|
261
|
-
sortDesc: false as boolean,
|
|
262
|
-
page: {
|
|
263
|
-
currentPage: 1,
|
|
264
|
-
perPage: 20
|
|
265
|
-
} as Page,
|
|
266
|
-
infoModal: {
|
|
267
|
-
id: 'info-modal',
|
|
268
|
-
title: '',
|
|
269
|
-
record: null
|
|
270
|
-
} as InfoModal
|
|
271
|
-
};
|
|
272
|
-
},
|
|
273
|
-
computed: {
|
|
274
|
-
...mapGetters([
|
|
275
|
-
'hasConsequences',
|
|
276
|
-
'hasCapice',
|
|
277
|
-
'getAnnotation',
|
|
278
|
-
'isAnnotationEnabled',
|
|
279
|
-
'isRecordsContainPhenotypes',
|
|
280
|
-
'isRecordsContainMvl',
|
|
281
|
-
'isSamplesContainInheritance',
|
|
282
|
-
'isSamplesContainDenovo',
|
|
283
|
-
'isSamplesContainDepth',
|
|
284
|
-
'isRecordsContainIncompletePenetrance',
|
|
285
|
-
'sampleMaternal',
|
|
286
|
-
'samplePaternal'
|
|
287
|
-
]),
|
|
288
|
-
...mapState([
|
|
289
|
-
'metadata',
|
|
290
|
-
'records',
|
|
291
|
-
'annotations',
|
|
292
|
-
'selectedSamplePhenotypes',
|
|
293
|
-
'filterRecordsByPhenotype',
|
|
294
|
-
'filterRecordsByInheritance',
|
|
295
|
-
'filterRecordsByDenovo',
|
|
296
|
-
'filterRecordsByDepth'
|
|
297
|
-
]),
|
|
298
|
-
genomeAssembly(): string {
|
|
299
|
-
return this.metadata.htsFile.genomeAssembly;
|
|
300
|
-
},
|
|
301
|
-
fields(): BvTableFieldArray {
|
|
302
|
-
// field keys must much report api field ids
|
|
303
|
-
const fields = [];
|
|
304
|
-
fields.push({ key: 'actions', label: '', class: ['compact', 'align-top'] });
|
|
305
|
-
fields.push({ key: 'p', label: 'pos', sortable: true });
|
|
306
|
-
fields.push({ key: 'r', label: 'ref' });
|
|
307
|
-
fields.push(this.sample ? { key: 's', label: 'sample' } : { key: 'a', label: 'alt' });
|
|
308
|
-
if (this.sample && this.samplePaternal !== null) {
|
|
309
|
-
fields.push({ key: 'father', label: 'father' });
|
|
310
|
-
}
|
|
311
|
-
if (this.sample && this.sampleMaternal !== null) {
|
|
312
|
-
fields.push({ key: 'mother', label: 'mother' });
|
|
313
|
-
}
|
|
314
|
-
if (this.hasCapice) {
|
|
315
|
-
fields.push({ key: 'capice', label: 'capice', sortable: true });
|
|
316
|
-
}
|
|
317
|
-
if (this.hasConsequences) {
|
|
318
|
-
fields.push({ key: 'expand', label: '', class: ['compact', 'align-top'] });
|
|
319
|
-
fields.push({ key: 'effect', label: 'effect' });
|
|
320
|
-
fields.push({ key: 'gene', label: 'symbol' });
|
|
321
|
-
if (this.isSamplesContainInheritance) {
|
|
322
|
-
fields.push({ key: 'inheritance', label: 'inheritance' });
|
|
323
|
-
}
|
|
324
|
-
fields.push({ key: 'hgvsC', label: 'hgvsc' });
|
|
325
|
-
fields.push({ key: 'hgvsP', label: 'hgvsp' });
|
|
326
|
-
fields.push({ key: 'gnomAD', label: 'gnomad' });
|
|
327
|
-
}
|
|
328
|
-
if (this.isRecordsContainMvl) {
|
|
329
|
-
fields.push({ key: 'mvl', label: 'mvl' });
|
|
330
|
-
}
|
|
331
|
-
if (this.hasConsequences) {
|
|
332
|
-
fields.push({ key: 'vkgl', label: 'vkgl' });
|
|
333
|
-
fields.push({ key: 'clinVar', label: 'clinvar' });
|
|
334
|
-
fields.push({ key: 'pubMed', label: 'pubmed' });
|
|
335
|
-
}
|
|
336
|
-
if (this.isAnnotationEnabled) {
|
|
337
|
-
fields.push({ key: 'geneMatch', label: 'geneMatch', class: 'input' });
|
|
338
|
-
fields.push({ key: 'class', label: 'class', class: 'input' });
|
|
339
|
-
fields.push({ key: 'txt', label: 'txt', class: 'input', thStyle: { minWidth: '20rem' } });
|
|
340
|
-
}
|
|
341
|
-
return fields;
|
|
342
|
-
}
|
|
343
|
-
},
|
|
344
|
-
methods: {
|
|
345
|
-
...mapActions(['loadRecords', 'selectRecord']),
|
|
346
|
-
provider(ctx: BvTableCtxObject): Promise<Row[]> {
|
|
347
|
-
const params: Api.Params = {
|
|
348
|
-
page: ctx.currentPage - 1,
|
|
349
|
-
size: ctx.perPage,
|
|
350
|
-
query: this.createQuery(),
|
|
351
|
-
sort: this.createSort(ctx)
|
|
352
|
-
};
|
|
353
|
-
|
|
354
|
-
return this.loadRecords(params).then(() => {
|
|
355
|
-
const records = this.records as Api.PagedItems<Vcf.Record>;
|
|
356
|
-
this.page.totalRows = records.page.totalElements;
|
|
357
|
-
this.page.totalPages = Math.ceil(records.page.totalElements / ctx.perPage);
|
|
358
|
-
return records.items.map(this.mapRecordToRow);
|
|
359
|
-
});
|
|
360
|
-
},
|
|
361
|
-
info(record: Vcf.Record, index: number, button: BButton): void {
|
|
362
|
-
this.infoModal.title = `Row index: ${index}`;
|
|
363
|
-
this.infoModal.record = record;
|
|
364
|
-
this.$root.$emit('bv::show::modal', this.infoModal.id, button);
|
|
365
|
-
},
|
|
366
|
-
resetInfoModal(): void {
|
|
367
|
-
this.infoModal.title = '';
|
|
368
|
-
this.infoModal.record = null;
|
|
369
|
-
},
|
|
370
|
-
createQuery(): Api.Query | Api.ComposedQuery | undefined {
|
|
371
|
-
const queries: (Api.Query | Api.ComposedQuery)[] = [];
|
|
372
|
-
if (this.sample) {
|
|
373
|
-
queries.push(this.createSampleQuery());
|
|
374
|
-
}
|
|
375
|
-
if (this.isRecordsContainPhenotypes && this.hasSamplePhenotypes() && this.filterRecordsByPhenotype) {
|
|
376
|
-
queries.push(this.createSamplePhenotypesQuery());
|
|
377
|
-
}
|
|
378
|
-
if (this.isSamplesContainInheritance && this.filterRecordsByInheritance) {
|
|
379
|
-
queries.push(this.createSampleInheritanceQuery());
|
|
380
|
-
}
|
|
381
|
-
if (this.isSamplesContainDenovo && this.filterRecordsByDenovo) {
|
|
382
|
-
queries.push(this.createSampleDenovoQuery());
|
|
383
|
-
}
|
|
384
|
-
if (this.isSamplesContainDepth && this.filterRecordsByDepth) {
|
|
385
|
-
queries.push(this.createSampleReadDepthQuery());
|
|
386
|
-
}
|
|
387
|
-
|
|
388
|
-
// todo: translate ctx filter param to query
|
|
389
|
-
|
|
390
|
-
let query: Api.Query | Api.ComposedQuery | undefined;
|
|
391
|
-
if (queries.length === 0) {
|
|
392
|
-
query = undefined;
|
|
393
|
-
} else if (queries.length === 1) {
|
|
394
|
-
query = queries[0];
|
|
395
|
-
} else {
|
|
396
|
-
query = {
|
|
397
|
-
operator: 'and',
|
|
398
|
-
args: queries
|
|
399
|
-
};
|
|
400
|
-
}
|
|
401
|
-
return query;
|
|
402
|
-
},
|
|
403
|
-
createSampleQuery(): Api.Query {
|
|
404
|
-
return {
|
|
405
|
-
selector: ['s', this.sample.index, 'GT', 't'],
|
|
406
|
-
operator: 'in',
|
|
407
|
-
args: ['het', 'hom_a', 'part']
|
|
408
|
-
};
|
|
409
|
-
},
|
|
410
|
-
createSampleInheritanceQuery(): Api.ComposedQuery {
|
|
411
|
-
return {
|
|
412
|
-
operator: 'or',
|
|
413
|
-
args: [
|
|
414
|
-
{
|
|
415
|
-
selector: ['s', this.sample.index, 'VIM'],
|
|
416
|
-
operator: '==',
|
|
417
|
-
args: 1
|
|
418
|
-
},
|
|
419
|
-
{
|
|
420
|
-
operator: 'and',
|
|
421
|
-
args: [
|
|
422
|
-
{
|
|
423
|
-
selector: getInheritanceModesGeneSelector(this.metadata.records),
|
|
424
|
-
operator: '!any_has_any',
|
|
425
|
-
args: ['AD', 'AR', 'XLR', 'XLD', 'XL']
|
|
426
|
-
},
|
|
427
|
-
{
|
|
428
|
-
selector: ['s', this.sample.index, 'VI'],
|
|
429
|
-
operator: 'has_any',
|
|
430
|
-
args: ['AD', 'AR', 'XLR', 'XLD', 'XL']
|
|
431
|
-
}
|
|
432
|
-
]
|
|
433
|
-
}
|
|
434
|
-
]
|
|
435
|
-
};
|
|
436
|
-
},
|
|
437
|
-
createSampleDenovoQuery(): Api.Query {
|
|
438
|
-
return {
|
|
439
|
-
selector: ['s', this.sample.index, 'VID'],
|
|
440
|
-
operator: '==',
|
|
441
|
-
args: 1
|
|
442
|
-
};
|
|
443
|
-
},
|
|
444
|
-
createSampleReadDepthQuery(): Api.Query {
|
|
445
|
-
return {
|
|
446
|
-
selector: ['s', this.sample.index, 'DP'],
|
|
447
|
-
operator: '>=',
|
|
448
|
-
args: 20
|
|
449
|
-
};
|
|
450
|
-
},
|
|
451
|
-
hasSamplePhenotypes(): boolean {
|
|
452
|
-
return this.selectedSamplePhenotypes !== null && this.selectedSamplePhenotypes.page.totalElements > 0;
|
|
453
|
-
},
|
|
454
|
-
createSamplePhenotypesQuery(): Api.Query {
|
|
455
|
-
const phenotypeIds = (this.selectedSamplePhenotypes.items as Api.Phenotype[])
|
|
456
|
-
.flatMap((phenotype) => phenotype.phenotypicFeaturesList)
|
|
457
|
-
.map((phenotypicFeature) => phenotypicFeature.type.id);
|
|
458
|
-
return {
|
|
459
|
-
selector: getPhenotypesSelector(this.metadata.records),
|
|
460
|
-
operator: 'any_has_any',
|
|
461
|
-
args: [...new Set(phenotypeIds)]
|
|
462
|
-
};
|
|
463
|
-
},
|
|
464
|
-
createSort(ctx: BvTableCtxObject): Api.SortOrder | undefined {
|
|
465
|
-
let sort: Api.SortOrder | undefined;
|
|
466
|
-
if (ctx.sortBy) {
|
|
467
|
-
switch (ctx.sortBy) {
|
|
468
|
-
case 'capice':
|
|
469
|
-
sort = {
|
|
470
|
-
property: ['n', 'CAP'],
|
|
471
|
-
compare: ctx.sortDesc
|
|
472
|
-
? (a, b) => {
|
|
473
|
-
if (a === null) {
|
|
474
|
-
return b === null ? 0 : 1;
|
|
475
|
-
} else if (b === null) {
|
|
476
|
-
return -1;
|
|
477
|
-
} else {
|
|
478
|
-
return Math.max(...(b as number[])) - Math.max(...(a as number[]));
|
|
479
|
-
}
|
|
480
|
-
}
|
|
481
|
-
: (a, b) => {
|
|
482
|
-
if (a === null) {
|
|
483
|
-
return b === null ? 0 : -1;
|
|
484
|
-
} else if (b === null) {
|
|
485
|
-
return 1;
|
|
486
|
-
} else {
|
|
487
|
-
return Math.max(...(a as number[])) - Math.max(...(b as number[]));
|
|
488
|
-
}
|
|
489
|
-
}
|
|
490
|
-
};
|
|
491
|
-
break;
|
|
492
|
-
case 'p':
|
|
493
|
-
// workaround for https://github.com/molgenis/vip-report-template/issues/73
|
|
494
|
-
sort = undefined;
|
|
495
|
-
break;
|
|
496
|
-
default:
|
|
497
|
-
sort = { property: ctx.sortBy, compare: ctx.sortDesc ? 'desc' : 'asc' };
|
|
498
|
-
break;
|
|
499
|
-
}
|
|
500
|
-
} else {
|
|
501
|
-
sort = undefined;
|
|
502
|
-
}
|
|
503
|
-
return sort;
|
|
504
|
-
},
|
|
505
|
-
mapRecordToRow(record: Vcf.Record) {
|
|
506
|
-
const row: Row = { ...record };
|
|
507
|
-
if (this.hasConsequences) {
|
|
508
|
-
const consequences: Consequences = getConsequences(record, this.metadata.records);
|
|
509
|
-
row.effect = {
|
|
510
|
-
metadata: consequences.metadata.effect,
|
|
511
|
-
items: consequences.items.map((consequence) => consequence.effect)
|
|
512
|
-
};
|
|
513
|
-
row.gene = {
|
|
514
|
-
metadata: {
|
|
515
|
-
id: 'GeneObject',
|
|
516
|
-
type: 'Other',
|
|
517
|
-
number: { type: 'NUMBER', count: 1 },
|
|
518
|
-
description: 'GeneObject'
|
|
519
|
-
},
|
|
520
|
-
items: consequences.items.map((consequence) =>
|
|
521
|
-
consequence.symbol !== null
|
|
522
|
-
? {
|
|
523
|
-
symbol: consequence.symbol,
|
|
524
|
-
incompletePenetrance: consequence.incompletePenetrance
|
|
525
|
-
}
|
|
526
|
-
: null
|
|
527
|
-
)
|
|
528
|
-
};
|
|
529
|
-
if (this.isSamplesContainInheritance) {
|
|
530
|
-
row.inheritance = {
|
|
531
|
-
metadata: consequences.metadata.inheritance,
|
|
532
|
-
items: consequences.items.map((consequence) => consequence.inheritance)
|
|
533
|
-
};
|
|
534
|
-
}
|
|
535
|
-
row.hgvsC = {
|
|
536
|
-
metadata: consequences.metadata.hgvsC,
|
|
537
|
-
items: consequences.items.map((consequence) => consequence.hgvsC)
|
|
538
|
-
};
|
|
539
|
-
row.hgvsP = {
|
|
540
|
-
metadata: consequences.metadata.hgvsP,
|
|
541
|
-
items: consequences.items.map((consequence) => consequence.hgvsP)
|
|
542
|
-
};
|
|
543
|
-
row.gnomAD = {
|
|
544
|
-
metadata: consequences.metadata.gnomAD,
|
|
545
|
-
items: consequences.items.map((consequence) =>
|
|
546
|
-
consequence.gnomAD !== null
|
|
547
|
-
? {
|
|
548
|
-
variant: getVariant(record, consequence),
|
|
549
|
-
gnomAD: consequence.gnomAD
|
|
550
|
-
}
|
|
551
|
-
: null
|
|
552
|
-
)
|
|
553
|
-
};
|
|
554
|
-
row.mvl = {
|
|
555
|
-
metadata: consequences.metadata.mvl,
|
|
556
|
-
items: consequences.items.map((consequence) => consequence.mvl)
|
|
557
|
-
};
|
|
558
|
-
row.vkgl = {
|
|
559
|
-
metadata: consequences.metadata.vkgl,
|
|
560
|
-
items: consequences.items.map((consequence) => consequence.vkgl)
|
|
561
|
-
};
|
|
562
|
-
row.clinVar = {
|
|
563
|
-
metadata: consequences.metadata.clinVar,
|
|
564
|
-
items: consequences.items.map((consequence) => consequence.clinVar)
|
|
565
|
-
};
|
|
566
|
-
row.pubMed = {
|
|
567
|
-
metadata: consequences.metadata.pubMed,
|
|
568
|
-
items: consequences.items.map((consequence) => consequence.pubMed)
|
|
569
|
-
};
|
|
570
|
-
row.expand = false;
|
|
571
|
-
}
|
|
572
|
-
if (this.isAnnotationEnabled) {
|
|
573
|
-
row.annotation = this.getAnnotation(record);
|
|
574
|
-
}
|
|
575
|
-
return row;
|
|
576
|
-
}
|
|
577
|
-
},
|
|
578
|
-
filters: { append, formatNumber },
|
|
579
|
-
watch: {
|
|
580
|
-
sample() {
|
|
581
|
-
this.page.currentPage = 1;
|
|
582
|
-
(this.$refs.table as BTable).refresh();
|
|
583
|
-
},
|
|
584
|
-
'$store.state.annotations': function () {
|
|
585
|
-
(this.$refs.table as BTable).refresh();
|
|
586
|
-
},
|
|
587
|
-
'$store.state.filterRecordsByPhenotype'() {
|
|
588
|
-
this.page.currentPage = 1;
|
|
589
|
-
(this.$refs.table as BTable).refresh();
|
|
590
|
-
},
|
|
591
|
-
'$store.state.filterRecordsByInheritance'() {
|
|
592
|
-
this.page.currentPage = 1;
|
|
593
|
-
(this.$refs.table as BTable).refresh();
|
|
594
|
-
},
|
|
595
|
-
'$store.state.filterRecordsByDenovo'() {
|
|
596
|
-
this.page.currentPage = 1;
|
|
597
|
-
(this.$refs.table as BTable).refresh();
|
|
598
|
-
},
|
|
599
|
-
'$store.state.filterRecordsByDepth'() {
|
|
600
|
-
this.page.currentPage = 1;
|
|
601
|
-
(this.$refs.table as BTable).refresh();
|
|
602
|
-
}
|
|
603
|
-
}
|
|
604
|
-
});
|
|
605
|
-
</script>
|