@molgenis/vip-report-template 2.7.3 → 3.0.0-beta

package/src/components/annotation/GeneMatchAnnotation.vue

@@ -1,33 +0,0 @@
-<template>
-  <b-form-select v-model="selected" :options="options" size="sm" @change="onChange" />
-</template>
-
-<script lang="ts">
-import Vue, { PropType } from 'vue';
-
-export default Vue.extend({
-  props: {
-    value: { type: String as PropType<string> }
-  },
-  data() {
-    return {
-      selected: this.value,
-      options: [
-        { value: null, text: '' },
-        { value: 'true', text: 'Yes' },
-        { value: 'false', text: 'No' }
-      ]
-    };
-  },
-  methods: {
-    onChange() {
-      this.$emit('update', this.selected);
-    }
-  },
-  watch: {
-    value(value) {
-      this.selected = value;
-    }
-  }
-});
-</script>

package/src/components/annotation/NotesAnnotation.vue

@@ -1,46 +0,0 @@
-<template>
-  <b-form-textarea
-    v-if="focus"
-    v-focus
-    size="sm"
-    v-model="text"
-    type="text"
-    debounce="500"
-    @blur="focus = false"
-    @update="onChange"
-  />
-  <b-form-input v-else size="sm" :value="text" type="text" debounce="500" @focus="focus = true" @update="onChange" />
-</template>
-
-<script lang="ts">
-import Vue, { PropType } from 'vue';
-
-export default Vue.extend({
-  props: {
-    value: { type: String as PropType<string> }
-  },
-  data() {
-    return {
-      text: this.value !== null ? this.value : '',
-      focus: false
-    };
-  },
-  methods: {
-    onChange() {
-      this.$emit('update', this.text);
-    }
-  },
-  watch: {
-    value(value) {
-      this.text = value;
-    }
-  },
-  directives: {
-    focus: {
-      inserted(el) {
-        el.focus();
-      }
-    }
-  }
-});
-</script>

package/src/globals/filters.ts

@@ -1,19 +0,0 @@
-const numberFormatWithGrouping = new Intl.NumberFormat('en-US', {
-  style: 'decimal',
-  maximumFractionDigits: 1
-});
-
-const numberFormatWithoutGrouping = new Intl.NumberFormat('en-US', {
-  style: 'decimal',
-  useGrouping: false,
-  maximumFractionDigits: 1
-});
-
-export const formatNumber = function (x: number, grouping = false): string {
-  const numberFormat = grouping ? numberFormatWithGrouping : numberFormatWithoutGrouping;
-  return numberFormat.format(x);
-};
-
-export const append = function (thisString: string, thatString: string): string {
-  return `${thatString}${thisString}`;
-};

package/src/globals/utils.ts

@@ -1,467 +0,0 @@
-import { Vcf, Api } from '@molgenis/vip-report-api';
-import { Consequence, ConsequenceMetadata, Consequences } from '@/types/Consequence';
-import { Variant } from '@/types/Variant';
-
-const consequenceMetadata: ConsequenceMetadata = {
-  effect: {
-    id: 'Consequence',
-    type: 'STRING',
-    number: { type: 'OTHER' },
-    description: 'Consequence'
-  },
-  symbol: { id: 'SYMBOL', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'SYMBOL' },
-  incompletePenetrance: {
-    id: 'IncompletePenetrance',
-    type: 'FLAG',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'IncompletePenetrance'
-  },
-  inheritance: {
-    id: 'InheritanceModesGene',
-    type: 'STRING',
-    number: { type: 'OTHER' },
-    description: 'InheritanceModesGene'
-  },
-  hgvsC: { id: 'hgvsC', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'hgvsC' },
-  hgvsP: { id: 'hgvsP', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'hgvsP' },
-  pubMed: {
-    id: 'PUBMED',
-    type: 'INTEGER',
-    number: { type: 'OTHER' },
-    description: 'Pubmed ID(s) of publications that cite existing variant'
-  },
-  clinVar: {
-    id: 'CLIN_SIG',
-    type: 'STRING',
-    number: { type: 'OTHER' },
-    description: 'ClinVar clinical significance of the dbSNP variant'
-  },
-  gnomAD: {
-    id: 'gnomAD_AF',
-    type: 'FLOAT',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'Frequency of existing variant in gnomAD exomes combined population'
-  },
-  mvl: {
-    id: 'VKGL_UMCG',
-    type: 'STRING',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'UMCG Managed variant list Classification'
-  },
-  vkgl: {
-    id: 'VKGL_CL',
-    type: 'STRING',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'VKGL public consensus'
-  }
-};
-
-function createConsequence(
-  info: Vcf.Value[],
-  effectIndex: number | undefined,
-  symbolIndex: number | undefined,
-  incompletePenetranceIndex: number | undefined,
-  inheritanceIndex: number | undefined,
-  hgvsCIndex: number | undefined,
-  hgvsPIndex: number | undefined,
-  pubMedIndex: number | undefined,
-  clinVarIndex: number | undefined,
-  gnomADIndex: number | undefined,
-  mvlIndex: number | undefined,
-  vkglIndex: number | undefined,
-  primaryIndex: number | undefined,
-  alleleIndexIndex: number | undefined
-): Consequence {
-  return {
-    effect: effectIndex !== undefined ? (info[effectIndex] as string[]) : [],
-    symbol: symbolIndex !== undefined ? (info[symbolIndex] as string | null) : null,
-    incompletePenetrance:
-      incompletePenetranceIndex !== undefined ? (info[incompletePenetranceIndex] as boolean) : false,
-    inheritance: inheritanceIndex !== undefined ? (info[inheritanceIndex] as string[]) : [],
-    hgvsC: hgvsCIndex !== undefined ? (info[hgvsCIndex] as string | null) : null,
-    hgvsP: hgvsPIndex !== undefined ? (info[hgvsPIndex] as string | null) : null,
-    pubMed: pubMedIndex !== undefined ? (info[pubMedIndex] as number[]) : [],
-    clinVar: clinVarIndex !== undefined ? (info[clinVarIndex] as string[]) : [],
-    gnomAD: gnomADIndex !== undefined ? (info[gnomADIndex] as number) : null,
-    mvl: mvlIndex !== undefined ? (info[mvlIndex] as string | null) : null,
-    vkgl: vkglIndex !== undefined ? (info[vkglIndex] as string | null) : null,
-    primary: primaryIndex !== undefined ? (info[primaryIndex] as string) : null,
-    alleleIndex: alleleIndexIndex != undefined ? (info[alleleIndexIndex] as number) : null
-  };
-}
-
-function createConsequences(
-  info: Vcf.Value[][],
-  effectIndex: number | undefined,
-  symbolIndex: number | undefined,
-  incompletePenetranceIndex: number | undefined,
-  inheritanceIndex: number | undefined,
-  hgvsCIndex: number | undefined,
-  hgvsPIndex: number | undefined,
-  pubMedIndex: number | undefined,
-  clinVarIndex: number | undefined,
-  gnomADIndex: number | undefined,
-  mvlIndex: number | undefined,
-  vkglIndex: number | undefined,
-  primaryIndex: number | undefined,
-  alleleIndexIndex: number | undefined
-): Consequence[] {
-  const items = [];
-  for (const item of info) {
-    const consequence = createConsequence(
-      item,
-      effectIndex,
-      symbolIndex,
-      incompletePenetranceIndex,
-      inheritanceIndex,
-      hgvsCIndex,
-      hgvsPIndex,
-      pubMedIndex,
-      clinVarIndex,
-      gnomADIndex,
-      mvlIndex,
-      vkglIndex,
-      primaryIndex,
-      alleleIndexIndex
-    );
-    items.push(consequence);
-  }
-
-  return items;
-}
-
-function getInfoConsequences(
-  infoMetadata: Vcf.InfoMetadata,
-  info: Vcf.Value[][],
-  effectId: string,
-  symbolId: string,
-  incompletePenetranceId: string | null,
-  inheritanceId: string | null,
-  hgvsCId: string,
-  hgvsPId: string,
-  pubMedId: string | null,
-  clinVarId: string | null,
-  gnomADId: string | null,
-  mvlId: string | null,
-  vkglId: string | null,
-  primaryId: string | null,
-  alleleIndexId: string | null
-): Consequence[] {
-  if (infoMetadata.nested === undefined) {
-    return [];
-  }
-
-  let effectIndex,
-    symbolIndex,
-    incompletePenetranceIndex,
-    inheritanceIndex,
-    hgvsCIndex,
-    hgvsPIndex,
-    pubMedIndex,
-    clinVarIndex,
-    gnomADIndex,
-    mvlIndex,
-    vkglIndex,
-    primaryIndex,
-    alleleIndexIndex;
-  let index = 0;
-  for (const nestedInfoMetadata of Object.values(infoMetadata.nested.items)) {
-    switch (nestedInfoMetadata.id) {
-      case effectId:
-        effectIndex = index;
-        break;
-      case symbolId:
-        symbolIndex = index;
-        break;
-      case incompletePenetranceId:
-        incompletePenetranceIndex = index;
-        break;
-      case inheritanceId:
-        inheritanceIndex = index;
-        break;
-      case hgvsCId:
-        hgvsCIndex = index;
-        break;
-      case hgvsPId:
-        hgvsPIndex = index;
-        break;
-      case pubMedId:
-        pubMedIndex = index;
-        break;
-      case clinVarId:
-        clinVarIndex = index;
-        break;
-      case gnomADId:
-        gnomADIndex = index;
-        break;
-      case mvlId:
-        mvlIndex = index;
-        break;
-      case vkglId:
-        vkglIndex = index;
-        break;
-      case primaryId:
-        primaryIndex = index;
-        break;
-      case alleleIndexId:
-        alleleIndexIndex = index;
-        break;
-      default:
-        break;
-    }
-    ++index;
-  }
-
-  return createConsequences(
-    info,
-    effectIndex,
-    symbolIndex,
-    incompletePenetranceIndex,
-    inheritanceIndex,
-    hgvsCIndex,
-    hgvsPIndex,
-    pubMedIndex,
-    clinVarIndex,
-    gnomADIndex,
-    mvlIndex,
-    vkglIndex,
-    primaryIndex,
-    alleleIndexIndex
-  );
-}
-
-function hasVepConsequences(metadata: Vcf.Metadata): boolean {
-  const csqInfo = metadata.info['CSQ'];
-  return csqInfo !== undefined;
-}
-
-function getVepConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Consequence[] {
-  const infoMetadata = metadata.info['CSQ'];
-  if (infoMetadata === undefined || record.n === undefined) {
-    return [];
-  }
-  const info = record.n;
-  if (!Object.prototype.hasOwnProperty.call(info, 'CSQ') && info.CSQ !== null) {
-    return [];
-  }
-  const csqInfo = info.CSQ as Vcf.Value[][];
-  return getInfoConsequences(
-    infoMetadata,
-    csqInfo,
-    'Consequence',
-    'SYMBOL',
-    'IncompletePenetrance',
-    'InheritanceModesGene',
-    'HGVSc',
-    'HGVSp',
-    'PUBMED',
-    'CLIN_SIG',
-    'gnomAD_AF',
-    'VKGL_UMCG',
-    'VKGL_CL',
-    'PICK',
-    'ALLELE_NUM'
-  );
-}
-
-function hasSnpEffConsequences(metadata: Vcf.Metadata): boolean {
-  const csqInfo = metadata.info['ANN'];
-  return csqInfo !== undefined;
-}
-
-function getSnpEffConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Consequence[] {
-  const infoMetadata = metadata.info['ANN'];
-  if (infoMetadata === undefined || record.n === undefined) {
-    return [];
-  }
-  const info = record.n;
-  if (!Object.prototype.hasOwnProperty.call(info, 'ANN') && info.ANN !== null) {
-    return [];
-  }
-  const annInfo = info.ANN as Vcf.Value[][];
-  return getInfoConsequences(
-    infoMetadata,
-    annInfo,
-    'Annotation',
-    'Gene_Name',
-    null,
-    null,
-    'HGVS.c',
-    'HGVS.p',
-    null,
-    null,
-    null,
-    null,
-    null,
-    null,
-    null
-  );
-}
-
-/**
- * Based on:
- * - http://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences
- * - http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf
- */
-const soTermRank: { [index: string]: number } = {
-  transcript_ablation: 0,
-  chromosome_number_variation: 1,
-  exon_loss_variant: 2,
-  splice_acceptor_variant: 3,
-  splice_donor_variant: 4,
-  stop_gained: 5,
-  frameshift_variant: 6,
-  stop_lost: 7,
-  start_lost: 8,
-  transcript_amplification: 9,
-  inframe_insertion: 10,
-  disruptive_inframe_insertion: 10,
-  conservative_inframe_insertion: 10,
-  inframe_deletion: 11,
-  disruptive_inframe_deletion: 11,
-  conservative_inframe_deletion: 11,
-  rare_amino_acid_variant: 12,
-  missense_variant: 13,
-  protein_altering_variant: 14,
-  splice_region_variant: 15,
-  splice_branch_variant: 15,
-  incomplete_terminal_codon_variant: 16,
-  start_retained_variant: 17,
-  initiator_codon_variant: 17,
-  stop_retained_variant: 18,
-  synonymous_variant: 19,
-  coding_sequence_variant: 20,
-  mature_miRNA_variant: 21,
-  '5_prime_UTR_variant': 22,
-  '5_prime_UTR_truncation': 22,
-  '5_prime_UTR_premature_start_codon_gain_variant': 22,
-  '3_prime_UTR_variant': 23,
-  '3_prime_UTR_truncation': 23,
-  non_coding_transcript_exon_variant: 24,
-  intron_variant: 25,
-  conserved_intron_variant: 25,
-  NMD_transcript_variant: 26,
-  non_coding_transcript_variant: 27,
-  upstream_gene_variant: 28,
-  downstream_gene_variant: 29,
-  TFBS_ablation: 30,
-  TFBS_amplification: 31,
-  TF_binding_site_variant: 32,
-  regulatory_region_variant: 32,
-  regulatory_region_ablation: 33,
-  regulatory_region_amplification: 34,
-  feature_elongation: 35,
-  feature_truncation: 36,
-  miRNA: 37,
-  custom: 38,
-  sequence_feature: 38,
-  intragenic_variant: 40,
-  conserved_intergenic_variant: 41,
-  intergenic_variant: 42,
-  intergenic_region: 43
-};
-
-function sortConsequences(thisConsequence: Consequence, thatConsequence: Consequence): number {
-  if (thisConsequence.primary === '1' && thatConsequence.primary !== '1') {
-    return -1;
-  } else if (thatConsequence.primary === '1') {
-    return 1;
-  } else {
-    let thisRank = Number.MAX_VALUE;
-
-    for (const soTerm of thisConsequence.effect) {
-      const rank = soTermRank[soTerm];
-      if (rank < thisRank) {
-        thisRank = rank;
-      }
-    }
-
-    let thatRank = Number.MAX_VALUE;
-    for (const soTerm of thatConsequence.effect) {
-      const rank = soTermRank[soTerm];
-      if (rank < thatRank) {
-        thatRank = rank;
-      }
-    }
-
-    return thisRank - thatRank;
-  }
-}
-
-/**
- * Returns consequences extracted from various info fields
- */
-export function getConsequences(record: Vcf.Record, recordMetadata: Vcf.Metadata): Consequences {
-  const consequences: Consequence[] = [];
-  if (hasVepConsequences(recordMetadata)) {
-    consequences.push(...getVepConsequences(record, recordMetadata));
-  }
-  if (hasSnpEffConsequences(recordMetadata)) {
-    consequences.push(...getSnpEffConsequences(record, recordMetadata));
-  }
-  consequences.sort(sortConsequences);
-  return { metadata: consequenceMetadata, items: consequences };
-}
-
-function getVepPhenotypesIndex(metadata: Vcf.Metadata): number | null {
-  const infoMetadata = metadata.info['CSQ'];
-  if (infoMetadata === undefined || infoMetadata.nested === undefined) {
-    return null;
-  }
-
-  let index = 0;
-  for (const nestedInfoMetadata of Object.values(infoMetadata.nested.items)) {
-    if (nestedInfoMetadata.id === 'HPO') {
-      return index;
-    }
-    ++index;
-  }
-  return null;
-}
-
-export function getPhenotypesSelector(recordMetadata: Vcf.Metadata): Api.Selector {
-  const index = getVepPhenotypesIndex(recordMetadata);
-  if (index === null) {
-    throw new Error('phenotypes unavailable');
-  }
-  return ['n', 'CSQ', '*', index];
-}
-
-function getVepInheritanceModesGeneIndex(metadata: Vcf.Metadata): number | null {
-  const infoMetadata = metadata.info['CSQ'];
-  if (infoMetadata === undefined || infoMetadata.nested === undefined) {
-    return null;
-  }
-
-  let index = 0;
-  for (const nestedInfoMetadata of Object.values(infoMetadata.nested.items)) {
-    if (nestedInfoMetadata.id === 'InheritanceModesGene') {
-      return index;
-    }
-    ++index;
-  }
-  return null;
-}
-
-export function getInheritanceModesGeneSelector(recordMetadata: Vcf.Metadata): Api.Selector {
-  const index = getVepInheritanceModesGeneIndex(recordMetadata);
-  if (index === null) {
-    throw new Error('inheritance modes gene unavailable');
-  }
-  return ['n', 'CSQ', '*', index];
-}
-
-export function getVariant(record: Vcf.Record, consequence: Consequence): Variant | null {
-  let variant;
-  if (consequence.alleleIndex !== null) {
-    variant = {
-      chr: record.c,
-      pos: record.p,
-      ref: record.r,
-      alt: record.a[consequence.alleleIndex - 1]
-    };
-  } else {
-    variant = null;
-  }
-  return variant;
-}

package/src/i18n.ts

@@ -1,23 +0,0 @@
-import Vue from 'vue';
-import VueI18n, { LocaleMessages } from 'vue-i18n';
-
-Vue.use(VueI18n);
-
-function loadLocaleMessages(): LocaleMessages {
-  const locales = require.context('./locales', true, /[A-Za-z0-9-_,\s]+\.json$/i);
-  const messages: LocaleMessages = {};
-  locales.keys().forEach((key) => {
-    const matched = key.match(/([A-Za-z0-9-_]+)\./i);
-    if (matched && matched.length > 1) {
-      const locale = matched[1];
-      messages[locale] = locales(key);
-    }
-  });
-  return messages;
-}
-
-export default new VueI18n({
-  locale: process.env.VUE_APP_I18N_LOCALE || 'en',
-  fallbackLocale: process.env.VUE_APP_I18N_FALLBACK_LOCALE || 'en',
-  messages: loadLocaleMessages()
-});

package/src/locales/en.json

@@ -1,82 +0,0 @@
-{
-  "brand": "VCF Report",
-  "about": "About",
-  "footer": "Report generated with {0} {1} (arguments: {2})",
-  "recordWarning": "The first {0} records are available out of a total of {1}.",
-  "sampleWarning": "The first {0} samples are available out of a total of {1}.",
-  "chr": "Chromosome",
-  "pos": "Position",
-  "id": "Identifiers",
-  "ref": "Reference",
-  "alt": "Alternates",
-  "qual": "Quality",
-  "filter": "Filters",
-  "info": "Info",
-  "format": "Format",
-  "type": "Type",
-  "capice": "CAPICE",
-  "effect": "Effect",
-  "symbol": "Gene",
-  "inheritance": "Gene Inh Modes",
-  "mvl": "MVL",
-  "vkgl": "VKGL",
-  "gnomad": "gnomAD",
-  "clinvar": "ClinVar",
-  "pubmed": "Literature",
-  "hgvsc": "HGVS C",
-  "hgvsp": "HGVS P",
-  "noSearchResults": "No Search Results",
-  "record": "record",
-  "records": "records",
-  "emptyTableMessage": "There are no records to show",
-  "clear": "Clear",
-  "sample": "Sample",
-  "samples": "Samples",
-  "father": "Father",
-  "mother": "Mother",
-  "pedigree": "Pedigree",
-  "phenotype": "Phenotype",
-  "phenotypes": "Phenotypes",
-  "phenotypesUnavailable": "no phenotype information available",
-  "vibe": "VIBE",
-  "recordDetails": "Record Details",
-  "ok": "Ok",
-  "prop": "Property",
-  "key": "Key",
-  "value": "Value",
-  "export": "Export",
-  "import": "Import",
-  "emptyFileError": "Import failed: file is empty",
-  "invalidFileHeaderError": "Import failed: invalid file header (expected: {0})",
-  "invalidFileLineError": "Import failed: invalid line in file",
-  "geneMatch": "Gene Y/N",
-  "class": "Class",
-  "txt": "Comments",
-  "annotations": "Notes",
-  "new": "New",
-  "open": "Open...",
-  "save": "Save...",
-  "exit": "Exit",
-  "matchPhenotype": "Only display records that match sample phenotype(s)",
-  "matchInheritance": "Only display records that match inheritance",
-  "matchDenovo": "Only display records that are denovo",
-  "matchDepth": "Only display records that have a read depth of 20 or higher",
-  "maleAffected": "Male, Affected.",
-  "maleUnaffected": "Male, Unaffected.",
-  "maleUnknown": "Male, Unknown affected status.",
-  "femaleAffected": "Female, Affected.",
-  "femaleUnaffected": "Female, Unaffected.",
-  "femaleUnknown": "Female, Unknown affected status.",
-  "sexUnknownAffected": "Unknown sex, Affected.",
-  "sexUnknownUnaffected": "Unknown sex, Unaffected.",
-  "sexUnknownAffectedUnknown": "Unknown sex, Unknown affected status.",
-  "allelicImbalance": "Allelic imbalance",
-  "lowReadDepth": "Read depth < 20",
-  "data": "Data",
-  "vcf": "VCF",
-  "genomeBrowserUnavailable": "Genome browser unavailable for selected record.",
-  "treeViewer": "Decision tree",
-  "missingDecisionTree": "Decision tree unavailable",
-  "treeInfo": "Click and drag in the tree to navigate, scroll to zoom.",
-  "incompletePenetrance": "Gene associated with incomplete penetrance."
-}

package/src/main.ts

@@ -1,22 +0,0 @@
-import Vue from 'vue';
-import './plugins/bootstrap-vue';
-import App from '@/App.vue';
-import i18n from '@/i18n';
-import router from '@/router';
-import store from '@/store/store';
-
-Vue.config.productionTip = false;
-Vue.config.errorHandler = (err) => {
-  console.error(err);
-  alert(err);
-};
-Vue.config.warnHandler = (msg) => {
-  console.warn(msg);
-  alert(msg);
-};
-new Vue({
-  i18n,
-  router,
-  store,
-  render: (h) => h(App)
-}).$mount('#app');