@molgenis/vip-report-template 2.6.3 → 2.7.2

package/src/components/Gene.vue

@@ -0,0 +1,32 @@
+<template>
+  <span>
+    <Anchor
+      :href="'https://www.omim.org/search?search=' + encodeURIComponent(value.symbol) + '&field=approved_gene_symbol'"
+      :text="value.symbol"
+    />
+    <b-button
+      pill
+      v-if="value.incompletePenetrance"
+      size="sm"
+      variant="info"
+      class="ml-2 p-0"
+      v-b-tooltip.click
+      :title="$t('incompletePenetrance')"
+    >
+      <sup>IP</sup>
+    </b-button>
+  </span>
+</template>
+
+<script lang="ts">
+import Vue, { PropType } from 'vue';
+import Anchor from '@/components/Anchor.vue';
+import { Gene } from '@/types/Gene';
+
+export default Vue.extend({
+  components: { Anchor },
+  props: {
+    value: { type: Object as PropType<Gene> }
+  }
+});
+</script>

package/src/components/RecordInfoDetailsItem.vue

@@ -1,11 +1,17 @@
 <template>
   <span v-if="metadata.number.type === 'NUMBER' && metadata.number.count === 1">
+    <span v-if="metadata.id === 'GeneObject'">
+      <Gene v-if="value.length > 0" :value="value" />
+    </span>
     <RecordInfoDetailsItemValue v-if="value !== null" :metadataId="metadata.id" :value="value" :details="details" />
   </span>
   <span v-else>
     <span v-if="metadata.id === 'PUBMED'">
       <PubMedAnchor v-if="value.length > 0" :pubMedIds="value" />
     </span>
+    <span v-else-if="metadata.id === 'GeneObject'">
+      <Gene v-if="value.length > 0" :value="value" />
+    </span>
     <span v-else>
       <span v-for="(item, index) in value" :key="index">
         <RecordInfoDetailsItemValue v-if="value !== null" :metadataId="metadata.id" :value="item" :details="details" />
@@ -20,9 +26,10 @@ import Vue, { PropType } from 'vue';
 import { Vcf } from '@molgenis/vip-report-api';
 import RecordInfoDetailsItemValue from '@/components/RecordInfoDetailsItemValue.vue';
 import PubMedAnchor from '@/components/PubMedAnchor.vue';
+import Gene from '@/components/Gene.vue';
 
 export default Vue.extend({
-  components: { PubMedAnchor, RecordInfoDetailsItemValue },
+  components: { Gene, PubMedAnchor, RecordInfoDetailsItemValue },
   props: {
     metadata: Object as PropType<Vcf.InfoMetadata>,
     value: [String, Number, Boolean, Array, Object] as PropType<

package/src/components/RecordInfoDetailsItemValue.vue

@@ -9,7 +9,10 @@
       :text="details ? value : value.replace(/_variant$/, '')"
     />
   </span>
-  <span v-else-if="metadataId === 'SYMBOL' || metadataId === 'Gene_Name'">
+  <span v-else-if="metadataId === 'GeneObject'">
+    <Gene :value="value" />
+  </span>
+  <span v-else-if="metadataId === 'Gene_Name'">
     <Anchor
       :href="'https://www.omim.org/search?search=' + encodeURIComponent(value) + '&field=approved_gene_symbol'"
       :text="value"
@@ -73,10 +76,11 @@
 <script lang="ts">
 import Vue, { PropType } from 'vue';
 import Anchor from '@/components/Anchor.vue';
+import Gene from '@/components/Gene.vue';
 import { mapState } from 'vuex';
 
 export default Vue.extend({
-  components: { Anchor },
+  components: { Anchor, Gene },
   props: {
     metadataId: String as PropType<string>,
     value: [String, Number, Boolean, Object] as PropType<string | number | boolean | unknown>,

package/src/components/RecordTable.vue

@@ -49,24 +49,24 @@
         <Genotype
           :genotype="data.item.s[sample.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[sample.index].f ? data.item.s[sample.index].f.DP : undefined"
-          :allelicDepth="data.item.s[sample.index].f ? data.item.s[sample.index].f.AD : undefined"
+          :readDepth="data.item.s[sample.index].DP"
+          :allelicDepth="data.item.s[sample.index].AD"
         />
       </template>
       <template v-slot:cell(father)="data">
         <Genotype
           :genotype="data.item.s[samplePaternal.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[samplePaternal.index].f ? data.item.s[samplePaternal.index].f.DP : undefined"
-          :allelicDepth="data.item.s[samplePaternal.index].f ? data.item.s[samplePaternal.index].f.AD : undefined"
+          :readDepth="data.item.s[samplePaternal.index].DP"
+          :allelicDepth="data.item.s[samplePaternal.index].AD"
         />
       </template>
       <template v-slot:cell(mother)="data">
         <Genotype
           :genotype="data.item.s[sampleMaternal.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[sampleMaternal.index].f ? data.item.s[sampleMaternal.index].f.DP : undefined"
-          :allelicDepth="data.item.s[sampleMaternal.index].f ? data.item.s[sampleMaternal.index].f.AD : undefined"
+          :readDepth="data.item.s[sampleMaternal.index].DP"
+          :allelicDepth="data.item.s[sampleMaternal.index].AD"
         />
       </template>
       <template v-slot:cell(expand)="data">
@@ -86,10 +86,10 @@
           :values="data.item.expand ? data.item.effect.items : data.item.effect.items.slice(0, 1)"
         />
       </template>
-      <template v-slot:cell(symbol)="data">
+      <template v-slot:cell(gene)="data">
         <RecordInfoDetailsItemMultiline
-          :metadata="data.item.symbol.metadata"
-          :values="data.item.expand ? data.item.symbol.items : data.item.symbol.items.slice(0, 1)"
+          :metadata="data.item.gene.metadata"
+          :values="data.item.expand ? data.item.gene.items : data.item.gene.items.slice(0, 1)"
         />
       </template>
       <template v-slot:cell(inheritance)="data">
@@ -229,7 +229,7 @@ interface Row {
   f: string[];
   s: Vcf.RecordSample[];
   effect?: unknown;
-  symbol?: unknown;
+  gene?: unknown;
   inheritance?: unknown;
   hgvsC?: unknown;
   hgvsP?: unknown;
@@ -281,6 +281,7 @@ export default Vue.extend({
       'isSamplesContainInheritance',
       'isSamplesContainDenovo',
       'isSamplesContainDepth',
+      'isRecordsContainIncompletePenetrance',
       'sampleMaternal',
       'samplePaternal'
     ]),
@@ -316,7 +317,7 @@ export default Vue.extend({
       if (this.hasConsequences) {
         fields.push({ key: 'expand', label: '', class: ['compact', 'align-top'] });
         fields.push({ key: 'effect', label: 'effect' });
-        fields.push({ key: 'symbol', label: 'symbol' });
+        fields.push({ key: 'gene', label: 'symbol' });
         if (this.isSamplesContainInheritance) {
           fields.push({ key: 'inheritance', label: 'inheritance' });
         }
@@ -509,9 +510,21 @@ export default Vue.extend({
           metadata: consequences.metadata.effect,
           items: consequences.items.map((consequence) => consequence.effect)
         };
-        row.symbol = {
-          metadata: consequences.metadata.symbol,
-          items: consequences.items.map((consequence) => consequence.symbol)
+        row.gene = {
+          metadata: {
+            id: 'GeneObject',
+            type: 'Other',
+            number: { type: 'NUMBER', count: 1 },
+            description: 'GeneObject'
+          },
+          items: consequences.items.map((consequence) =>
+            consequence.symbol !== null
+              ? {
+                  symbol: consequence.symbol,
+                  incompletePenetrance: consequence.incompletePenetrance
+                }
+              : null
+          )
         };
         if (this.isSamplesContainInheritance) {
           row.inheritance = {

package/src/globals/utils.ts

@@ -10,6 +10,12 @@ const consequenceMetadata: ConsequenceMetadata = {
     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',
@@ -54,6 +60,7 @@ function createConsequence(
   info: Vcf.Value[],
   effectIndex: number | undefined,
   symbolIndex: number | undefined,
+  incompletePenetranceIndex: number | undefined,
   inheritanceIndex: number | undefined,
   hgvsCIndex: number | undefined,
   hgvsPIndex: number | undefined,
@@ -68,6 +75,8 @@ function createConsequence(
   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,
@@ -85,6 +94,7 @@ function createConsequences(
   info: Vcf.Value[][],
   effectIndex: number | undefined,
   symbolIndex: number | undefined,
+  incompletePenetranceIndex: number | undefined,
   inheritanceIndex: number | undefined,
   hgvsCIndex: number | undefined,
   hgvsPIndex: number | undefined,
@@ -102,6 +112,7 @@ function createConsequences(
       item,
       effectIndex,
       symbolIndex,
+      incompletePenetranceIndex,
       inheritanceIndex,
       hgvsCIndex,
       hgvsPIndex,
@@ -124,6 +135,7 @@ function getInfoConsequences(
   info: Vcf.Value[][],
   effectId: string,
   symbolId: string,
+  incompletePenetranceId: string | null,
   inheritanceId: string | null,
   hgvsCId: string,
   hgvsPId: string,
@@ -141,6 +153,7 @@ function getInfoConsequences(
 
   let effectIndex,
     symbolIndex,
+    incompletePenetranceIndex,
     inheritanceIndex,
     hgvsCIndex,
     hgvsPIndex,
@@ -160,6 +173,9 @@ function getInfoConsequences(
       case symbolId:
         symbolIndex = index;
         break;
+      case incompletePenetranceId:
+        incompletePenetranceIndex = index;
+        break;
       case inheritanceId:
         inheritanceIndex = index;
         break;
@@ -200,6 +216,7 @@ function getInfoConsequences(
     info,
     effectIndex,
     symbolIndex,
+    incompletePenetranceIndex,
     inheritanceIndex,
     hgvsCIndex,
     hgvsPIndex,
@@ -233,6 +250,7 @@ function getVepConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Consequ
     csqInfo,
     'Consequence',
     'SYMBOL',
+    'IncompletePenetrance',
     'InheritanceModesGene',
     'HGVSc',
     'HGVSp',
@@ -267,6 +285,7 @@ function getSnpEffConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Cons
     'Annotation',
     'Gene_Name',
     null,
+    null,
     'HGVS.c',
     'HGVS.p',
     null,

package/src/locales/en.json

@@ -77,5 +77,6 @@
   "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."
+  "treeInfo": "Click and drag in the tree to navigate, scroll to zoom.",
+  "incompletePenetrance": "Gene associated with incomplete penetrance."
 }

package/src/mocks/apiDataMock.ts

@@ -102,7 +102,7 @@ export const apiData: ApiData.Container = {
   },
   base85: {
     vcfGz:
-      'ABzY800000008Y>>2o4Svi~gq6@(lize7M}-KDp31V$30wJr-r9)BVj)M9um0S}PZvr&Ki%j}z`xisTrXC!;1KC+?mmsxq$(cgaiFnkOi#?z<X{P?bU_N%P%Z@&HZ?EIp0dVBo0^ONJ7M!S7@63qJ3;bcA>kB;{nkB=36Y935yl}T?l3-0&7r)REjFB_fknUkBttLLZp!SomoJ0B;(@%d;T41#Ilb0(AN__rZ`b5NNEz5B|2Fqwa-{0AM+D*qhf@#Rm)T&c=<8lApJA|jtvdeb0oLva6}#jkI53SZxzPluzy;<vYg(RhwGix1zOClA+FKin8qg3<F+FzwNKW&BW?jAygq`^TU%9DN9;!+CGi4=PXN`(RdE{)Xl@@SNv9s5yR`jGssMmD#*Ee=hsTlU+aZ1o{7Uy!r!MTfl%A2C<}iqeaep^ZtjDPrcl=nV0lIi>(aBPHKA`{MLJ#JO<rggGu+-{zGpx8rLGNsC|5TMB4MKv+MAin~hW@8__qPJ&t?x#qUL;^X4h)^!&qk5R8WX;rwG|f*LmLhhqMZhw1pKQXfpm&y!jG`Kdps4*LE2{At3Vj=KE6L4Q80qtKrpd(-Y{FzZf+li+bU3hLA6(X5ULj_bej8n3bXG?+a<&ZBGH=voa~s15$rO>XfnF@&54c-ZevhW(%};{%SgCC^4(A>+FJ(-u-}jz_cL|DFSaJN`zzKC6V>p5ncy_m7pk)0<l5EVL6x6|?}sW8iZS`t!@1MziDFzg+%sec?$l{8@lPn+9F#Wyy*E;rzPu%gw1jeRqB3&#yYS_~%XQuH6rRPkjI6s?o*HG^958=1Ds{xtWgV!ElsaXgm!^<8H4%yq{rP?y)ug^ta(`jvRJ>?M;Whi0b0v^y0L8_4d-AoVPoTtLCY1cWxV3C;sfB(Q11X`j2tLyY1_@w|M_e>#Es3Kk>JxXYJFUx~RX+H_6HM8UE>n%}tI6qw!PYq}w>lj&Ad3mkVd@zvs?Q8|~cL+4)uO?CR_^cXr)*lRIli&owXbiS~KRx3960=S_d}=Je{?-@N_d^7O<v-<&po>|(opu1j5#Q3?fg_hah<8`q2unitXE)7wV-@@+dhxp<r0zWVVzI=F3|{BZsDq<fj(!h=?N^fo%W!^1^oygR>X7W!bBHX<21g8pzuJ#Ib?f=d4poy_oI*bn6yeP{_g#}_DiGQ~?4xPtzzGXD@%uu}*4^zHZ=eaK1+GNs$K`RrFDZI2)3|3qgKa)6KH=N;am<D;gEnyHDy6YQVI`<!v8GF9ce!pxCy`-f<<pL(PF3+(;ZA#1ba{r(uu-EZ^bzx5x7{eRT@<7rT9M%OCi_hddQy?KTGW**FgkPl!au<t9ODv##fu)%+r^%333l9td^9(qs1$B$8i{?;9iYaQg^{QBo<Z!!s{l~M00IR5TMExqr}dr?d2S8Wp9e;3N|_`B(M=yLnxdsLX?@7{LKs`k6@lZKFmIYwFxBkrI3!F_jvf}T%F1J<+;PiD~<k^<L9<5BLp@LD&2Z9WXTq(HN7FhafjSC?eYfGbj!wXOU|@bRDH>HTpdHLmDY#{B?8r`fTrpza-arq59%f_C<J|5spgzcL>_Eo)Y&T$O&W{{ipiScvU(9iOk`)AbMIr*U_Nz9JaSP^J%PsOfsQb=&+P%s#d<q^}Og$9TC0_u~C~9i*2Zo=1ITHoW%$ePc9F?nU&y2e|KN^r^WG@0z|e?|D!G#u$Fe_zC&kpM2=e0<m9dUbipLo5%Z(<1q^Tt~U+2L@4(wZ(5fpRkU6gL_rr32MRIqJ3eB(5jMUy0sNTz_w6f$3KUWdLd+46*6CIA`sB0%F1#4Le;z*G(+2@!NQ9yBJl>!38th}t_V{t~0lC~K?Z$79aEiXT3XCuZbHv1v<dtfr)jaDm`T@yQjjL|foNmbFuwNTIJkZAs;xC38+pnPQnji1eZxwzGN%{PyOSUaG635lypAuG-bnR-t^2eJP=*BkwV?8nbRf4DXzccJB)$yO(q-FA)1QTb#@TQ>au}?jwg9;ub=DXm=Y6)%gA|mZmFg2Pz&o(^}`{(GX_+-;F<i?{1=x7r)y84J14>r-}qk-t5_)7h9i*F($8$CrwTTs7Eso!p*zDrwlx4tFhm4}1S!^7cYFdEE19CPWoVw%HYYJJ`d^Zg<<U$~h)D!@5mM1fkAQiHRM<0Gs<Ei(c@8^?`a*AkUdTjoG<&DK%tl-dA(IMZewb=FknKv=ECI%=CzOD(iS-qumOj2buyL~b25u#{XVC8UvS8xBy8xKNB~1-eMiSC9*<z&ceVUm;JxPj=SWB6%iIW`uM~t`!kv5@lQo5N<7wpi3L$m{8KFq9#I0U;&)MC}!<v+tSZAmKnq45}&S=8dZl|XNxW2sYJCvJ{4cv5?(G)X@R?C0iot4Uk-vvrPubLcjeN=CK;x5v3LHG@r50I!$)6s%0F8x?TD1Z=rD_*u!9NCV)v4`meBLW*OGvt^3sT*5MU=>|Mz#XpEa@=KTk1yt|Q0~!$Gb8FsM`~mCuxLRI2}|R3E<iw)y7v`f~5)y1jRPvWGeJUgM&(_tV?P#a>h$-J{HQFRE_s-JmzYv|#UYjCtmC@2p3EzJWc9ipPNM)%Kcu9sEtz)V*fo2IB>kw)&rD`={fMe;Urn_XpkBN%>0*Vs9IrQ-9OA{n2;;0m^qU35gPAe|3qGC;%72m>Tz!xH1wY9^TZAFOVGdYf|gx_Z@$A6J7^xrK`cwq}G@YK<UnO;uT1bR31<LZT)B891QB6!N5;v8nCZx#}6=gzf)FOjDfLPp8ofzVLB966zGT7&`AWCvUuigO&bv(tC|!hK8Bi6Ha=$FvjYhKdEdD8{_br%{Gjmf;Y-oM_VSuq4NY{vfQths5Ud4I41WPA@cW|jKU7RP?(DTXM<+K&cjx&33I4m>!zYduJ8GO9!4Ya*y><lUXQ^&V)XG+?+1zU_s;4v%YG>6CM-NlXn7jAEV-Qx<ei!XD(3M8ucPwk@&2$XP(k%t9ivG$Ybrq>mD5i?HeCwv(@`C}gF|Q8>a}<uz(i$Uxuh3FmGdhKu{*yHgF1k{Say%W0!N&sdH$M7>5;%M*D%)#i0gqHOb6^-#RmQyl4EVfgd=_m4#w12Mw#-yA3?nz1%B#z(Mh85y%J{N2a%YUOH7G)_>dF^L5Pf7mvz6RR!%Si;IWuGykkTWS$J2sY0Lh)UVBA6T61XvFH&&o7YH4@pHR~WJ0bN6B=J40t;ni$p0zVBc1J}TW)8c?*8#(7LJ`g0RiyQhsItcCP{rI1w88)Ez6xOlw2%evvpWbeRpj+<G>CXz*4SJQ54)_N%|1!Pd+*nhSE0rd`zo;=rXf6{klBf&lUDf5!1nl$lXv%XqsIW&DybH$bHtf-@HIiwcy!pXv;n<Qg3gogTmd&X3`THamC0gG%qmIm-gHS9e5DvB-Oua_OjwBvW{m=EbpSK3}c{3CXCYa>k9YeV=6rGmIfgtHr%Q|%W^EmuR@c6M?kU-?iPhyPGc!roSU>yUz$MSzNEFC%Py+#pB7Gc@=ow1aeQB1KU6$jJ&I72Ksb|O@9AQf+-iuX~)`-mlGHC!sGBNYcGWeBRn)HDj7@G-57W-kGj9ngOe;hQ3y0$dL7!k-9UrLaL|&Iglu7dxNX<Z;+Xmp>kjrzym5&RcJGhSy7U`HS#MF8&)@-#1cgDjX)Z+%k30Y-0{;jHCn2nX?&cO0Gr?Y8W&uxb-N;%sY0}<^@Ypgp;Z=)@pqKMr-4=!2=8&t-=E>nKFVMU?10tJ9z-;zl9TGK?Wp-l{#*dKZy{4>2e`RyD<XTRS0rf$0cwQK|#l76A-pB8+nXSyreKnSbtK#@~z&y-ssIe>9w$2r*c7OvW1!OG17}lyR5Ttq-43yf>Grr0bFbnX7ll+JLqAqd;c<3EkQ|0QECYQR0pl9Kp%!A7y>J_1pkGWpof;AM}erKAt7c}Y)es#QcdO-Rw8C<PLU?-f+lC#QbC1d1@@VaO2yGHtD<VIG!H!a6G3e-oEHdkrwFyuOnr9i%a<_+DH_X|&nD8|^&Z3Q6e+wUy}a{-M!!DjM7Ea(DTS4x?X@7>N|0qu6tVzHRgE(V@MJIqN0+%|g%6%b{a`vrE$hyPgHc#sr&%FU+<}oJS_gYT$+8lL<z%pAp|fD4wG?m=fJd+pXRN%0QbWmO2hpaqgGkV;I>^lphJ)z-?UJyV09F<aI-kE!W<){SK~RK{6<UBgh}39C6ly2_TkIepjHQwzIY{ip7|2B(1P!dxYfOD88!owy%{mv5Ns+E#$AcBo;X!s-FZZuWZ{o^Guo@*vOlbxOTqxlb#*|KD^NcxgXd<~l=Ro5M63{1LN{gvHK7*+~=TaXa0X7FP4psPh7z7+}gK*>3D7Cza9C!HZa3}cy2Gg3!<s60AwJ(r_U5e)_VnQ>c6G2H!a*BEtr(X3UF}+HuR7ye%?bNcARBH87l0sjiu^URRK67{aTI94<EG(5lsDPK6O|v?#xP06B<qgWgmDB<;U<3op5_fe-J7z)?W^F1HIYUz|be3#561lYk6E}t7sVj(FSz|1>VTggk!GxP)4JGhrmAEAevKU>^f1<{96k+7VyE3&)#R(cDa}K5EjG&Aj572L-VDUgWDFj_XwZx1rlu<0A)qQCrw0sL_c?_*BK$}&zI18a=4xzQ^w%IGR82N1htyrP8Hib6UTBcvMHiJ!W0j*pCtt&ul#H&F_230J2jrGtbGzhH`xl%W9ur4zQ(h#&5v?ILE<LU0u!WV@tcLG0tJ+=uAVar&47y<Fk)K<vIk7<uo9#6k=wGCl|Euf7<1Zx+e<t&3X^kar<yB7VJV6V`E<6A%*g$Tm90<>BF%0r7_(a0i|$J1A6p)8dFRtMt?L`6pyVk?U=!fRxkhfQyxwt9uys)E`YOyytIHc6vZi666dNQc7{8iE#beoP318Da`8lS$HmRH*mz6<V!e3uvJnTFVO18mV5PMc9Dj&vL0evj#Ci7}KVp3N2J-Vr7V^!zYjg1KKYT(T%e_-rSsAcq=ghC?bsCr}T1tJ2$~&JwAd!{R={r{2)5CpetglJ5QPK2EXCuC7@QQ;%yfs#+4LLJq>65?(J2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     fastaGz: {
       '1:10042288-10042788':
         'ABzY800000002#qTMEKZ3`GCC7ojbJmwpH#AKAd{e=X)rs#sd@Bbi6W_i-Kj{yfjM9^Smx+9Larlo`ELg<l1~z3r8!GUQJ0m8ym)8U`}CE7g=s>8808G~E!>54$YrvcZ(-L#$VpmdhA9B{jC$1ds_c=59}2<_dJ*g<OWidWM*zjL2IkV8;uzj1g9GufGD*XpWdclZc##2HWWTs+BF8P=j=ugvRU~z|$)$)-To>Kk^RtKZLTEbcW-=QQY~_Iit)WY}kGW$@poJA~D%3|Je2cTbQ393jzQD',

package/src/store/getters.ts

@@ -20,12 +20,14 @@ export default {
       return 0;
     });
   },
-  getSampleById: (state: State) => (id: string): Api.Sample | null => {
-    if (state.samples === null) {
-      return null;
-    }
-    return state.samples.items.find((sample) => sample.person.individualId === id) || null;
-  },
+  getSampleById:
+    (state: State) =>
+    (id: string): Api.Sample | null => {
+      if (state.samples === null) {
+        return null;
+      }
+      return state.samples.items.find((sample) => sample.person.individualId === id) || null;
+    },
   sampleMaternal: (state: State): Api.Sample | null => {
     if (state.selectedSample === null) {
       return null;
@@ -94,31 +96,33 @@ export default {
   isAnnotationEnabled: (state: State): boolean => {
     return state.annotations !== null;
   },
-  getAnnotation: (state: State) => (record: Vcf.Record): Annotation => {
-    if (state.annotations === null) {
-      throw 'Annotations disabled';
-    }
-    if (state.selectedSample == null) {
-      throw 'No sample selected';
-    }
+  getAnnotation:
+    (state: State) =>
+    (record: Vcf.Record): Annotation => {
+      if (state.annotations === null) {
+        throw 'Annotations disabled';
+      }
+      if (state.selectedSample == null) {
+        throw 'No sample selected';
+      }
 
-    const sampleId = state.selectedSample.person.individualId;
-    const key = `${sampleId}_${record.c}_${record.p}_${record.r}_${record.a.join(',')}`;
-    let annotation = state.annotations[key];
-    if (annotation === undefined) {
-      annotation = {
-        sampleId: sampleId,
-        chr: record.c,
-        pos: record.p,
-        ref: record.r,
-        alt: record.a,
-        geneMatch: null,
-        class: null,
-        txt: null
-      };
-    }
-    return annotation;
-  },
+      const sampleId = state.selectedSample.person.individualId;
+      const key = `${sampleId}_${record.c}_${record.p}_${record.r}_${record.a.join(',')}`;
+      let annotation = state.annotations[key];
+      if (annotation === undefined) {
+        annotation = {
+          sampleId: sampleId,
+          chr: record.c,
+          pos: record.p,
+          ref: record.r,
+          alt: record.a,
+          geneMatch: null,
+          class: null,
+          txt: null
+        };
+      }
+      return annotation;
+    },
   /**
    * Returns whether records contain mvl annotations.
    */
@@ -200,4 +204,4 @@ export default {
     }
     return hasReadDepth;
   }
-};
+};

package/src/types/Consequence.ts

@@ -3,6 +3,7 @@ import { Vcf } from '@molgenis/vip-report-api';
 export interface ConsequenceMetadata {
   effect: Vcf.InfoMetadata;
   symbol: Vcf.InfoMetadata;
+  incompletePenetrance: Vcf.InfoMetadata;
   inheritance: Vcf.InfoMetadata;
   hgvsC: Vcf.InfoMetadata;
   hgvsP: Vcf.InfoMetadata;
@@ -17,6 +18,7 @@ export interface Consequence {
   alleleIndex: number | null;
   effect: string[];
   symbol: string | null;
+  incompletePenetrance: boolean | false;
   inheritance: string[];
   hgvsC: string | null;
   hgvsP: string | null;

package/src/types/DecisionTree.d.ts

@@ -32,8 +32,8 @@ type CategoricalNode = {
   outcomeMap: {
     [key: string]: Outcome;
   };
-  outcomeMissing: Outcome;
-  outcomeDefault: Outcome;
+  outcomeMissing?: Outcome;
+  outcomeDefault?: Outcome;
 };
 
 type ExitNode = {

package/src/types/Gene.ts

@@ -0,0 +1,4 @@
+export interface Gene {
+  symbol: string | null;
+  incompletePenetrance: boolean | false;
+}

package/src/utils/treeBuilder.ts

@@ -63,19 +63,34 @@ export const retrieveEdges = (inputTree: DecisionTree): TreeEdgesArray => {
   let edges: TreeEdgesObj = {};
   Object.keys(inputTree.nodes).forEach((key) => {
     const node: Node = inputTree.nodes[key];
-    if ('outcomeTrue' in node) {
-      edges = createSimpleEdge('True', node, key, edges);
-      edges = createSimpleEdge('False', node, key, edges);
-      if ('outcomeMissing' in node) {
-        edges = createSimpleEdge('Missing', node, key, edges);
-      }
-    } else if ('outcomeMap' in node) {
-      Object.keys(node.outcomeMap).forEach((category) => {
-        const nextNode = node.outcomeMap[category].nextNode;
-        edges = createEdge(nextNode, category, key, edges);
-      });
-      edges = createSimpleEdge('Missing', node, key, edges);
-      edges = createSimpleEdge('Default', node, key, edges);
+    switch (node.type) {
+      case 'BOOL':
+        edges = createSimpleEdge('True', node, key, edges);
+        edges = createSimpleEdge('False', node, key, edges);
+        if ('outcomeMissing' in node) {
+          edges = createSimpleEdge('Missing', node, key, edges);
+        }
+        break;
+      case 'CATEGORICAL':
+        Object.keys(node.outcomeMap).forEach((category) => {
+          const nextNode = node.outcomeMap[category].nextNode;
+          edges = createEdge(nextNode, category, key, edges);
+        });
+        if ('outcomeMissing' in node) {
+          edges = createSimpleEdge('Missing', node, key, edges);
+        }
+        if ('outcomeDefault' in node) {
+          edges = createSimpleEdge('Default', node, key, edges);
+        }
+        break;
+      case 'EXISTS':
+        edges = createSimpleEdge('True', node, key, edges);
+        edges = createSimpleEdge('False', node, key, edges);
+        break;
+      case 'LEAF':
+        break;
+      default:
+        throw new Error('unknown node type');
     }
   });
   return Object.keys(edges).map((k) => edges[k]);

package/tests/unit/globals/utils.spec.ts

@@ -6,6 +6,12 @@ import { Consequence } from '@/types/Consequence';
 const expectedMetadata = {
   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',
@@ -169,6 +175,7 @@ test('get consequences in case of CSQ info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -183,6 +190,7 @@ test('get consequences in case of CSQ info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -243,6 +251,7 @@ test('get consequences in case of CSQ info with extended info', () => {
         gnomAD: 0.1234,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: ['12345678', '23456789'],
         clinVar: ['likely_pathogenic', 'pathogenic'],
         vkgl: 'B',
@@ -257,6 +266,7 @@ test('get consequences in case of CSQ info with extended info', () => {
         gnomAD: 0.2345,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: ['12345678'],
         clinVar: ['benign'],
         vkgl: 'VUS',
@@ -289,6 +299,7 @@ test('get consequences in case of ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -303,6 +314,7 @@ test('get consequences in case of ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -336,6 +348,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC1',
         hgvsP: 'hgvsP1',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -350,6 +363,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC0',
         hgvsP: 'hgvsP0',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,
@@ -364,6 +378,7 @@ test('get consequences in case of CSQ and ANN info', () => {
         gnomAD: null,
         hgvsC: 'hgvsC2',
         hgvsP: 'hgvsP2',
+        incompletePenetrance: false,
         pubMed: [],
         clinVar: [],
         mvl: null,

package/tests/unit/store/getters.spec.ts

@@ -517,7 +517,7 @@ test('whether records contain MVL annotations - no meta', () => {
 
 test('whether records contain MVL annotations - no info meta', () => {
   const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { };
+  recordsMetadata.info = {};
 
   const metadata = mock<Api.Metadata>();
   metadata.records = recordsMetadata;