diff --git a/src/webcomponents/variant/custom/steiner-report.js b/src/webcomponents/variant/custom/steiner-report.js
index 35342af8b9..85b2efd6c9 100644
--- a/src/webcomponents/variant/custom/steiner-report.js
+++ b/src/webcomponents/variant/custom/steiner-report.js
@@ -291,13 +291,6 @@ class SteinerReport extends LitElement {
}
}
- onFieldChange() {
- this._data = {
- ...this._data,
- };
- this.requestUpdate();
- }
-
onSignatureChange(event, type) {
this.selectedSignatures[type] = event.detail.value;
this._config = {
@@ -365,7 +358,6 @@ class SteinerReport extends LitElement {
diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js
index 5efa87051b..5602f9ea25 100644
--- a/src/webcomponents/variant/variant-browser-grid.js
+++ b/src/webcomponents/variant/variant-browser-grid.js
@@ -211,6 +211,34 @@ export default class VariantBrowserGrid extends LitElement {
// summary: !this.query.sample && !this.query.family,
...this.query
};
+
+ // TASK-5791: Temporary SNP ID Search fix
+ if (this.query.xref) {
+ const snpIds = this.query.xref.split(",").filter(xref => xref.startsWith("rs"));
+ if (snpIds.length > 0) {
+ const snpRegion = [];
+ const request = new XMLHttpRequest();
+ for (const snpId of snpIds) {
+ const url = `https://rest.ensembl.org/variation/human/${snpId}?content-type=application/json`;
+
+ request.onload = event => {
+ if (request.status === 200) {
+ const restObject = JSON.parse(event.currentTarget.response);
+ const mapping = restObject.mappings?.find(m => m.assembly_name === "GRCh38");
+ snpRegion.push(mapping.seq_region_name + ":" + mapping.start);
+ }
+ };
+ request.open("GET", url, false);
+ request.send();
+ }
+ if (this.filters.region) {
+ this.filters.region += "," + snpRegion.join(",");
+ } else {
+ this.filters.region = snpRegion.join(",");
+ }
+ }
+ }
+
this.opencgaSession.opencgaClient.variants().query(this.filters)
.then(res => {
// FIXME A quick temporary fix -> TASK-947
@@ -1060,7 +1088,6 @@ export default class VariantBrowserGrid extends LitElement {
-
`;
}
diff --git a/src/webcomponents/variant/variant-utils.js b/src/webcomponents/variant/variant-utils.js
index f9a07f9767..bf5cf791a7 100644
--- a/src/webcomponents/variant/variant-utils.js
+++ b/src/webcomponents/variant/variant-utils.js
@@ -21,42 +21,9 @@ import VariantGridFormatter from "./variant-grid-formatter.js";
export default class VariantUtils {
- static jsonToTabConvert(variants, studiesPopFrequencies, samples, nucleotideGenotype, fieldList) {
+ static jsonToTabConvert(variants, populationFrequenciesStudies, samples, nucleotideGenotype, fieldList) {
const rows = [];
let populationMap = {};
- const headerString = [];
- // const sampleIds = samples?.map(sample => sample.id);
-
- // took from the first result. Is there a better way?
- // allele count / allele freqs
- const cohortAlleleStatsColumns = [];
- const alleleStats = [];
- const studyIds = [];
-
- // Code to Remove
- // ###
- if (variants[0].studies?.length) {
- variants[0].studies.forEach(study => {
- if (study.studyId.includes("@")) {
- const studyId = study.studyId.split(":")[1];
- studyIds.push(studyId);
- cohortAlleleStatsColumns.push(`cohorts.${studyId}.alleleCount`, `cohorts.${studyId}.altAlleleFreq`);
- // alleleCount, altAlleleFreq
-
- // cohort ALL is always the first element in study.stats
- // Remove
- alleleStats.push({
- id: studyId,
- stats: study.stats,
- });
- } else {
- console.error("Unexpected studyId format");
- }
- });
- }
- // #####
-
- const popStudyIds = studiesPopFrequencies?.map(study => "popfreq." + study.id);
/* // explicit list gives less maintainability but we need customisation (also in some cases for each column there is more than 1 field) */
let flatFieldList = [];
@@ -66,11 +33,12 @@ export default class VariantUtils {
// default list
flatFieldList = [
"id",
+ "snpId",
"gene",
"type",
- // Adding SAMPLES (includeSample=all in VB and Case samples in Sample VB)
- ...samples.map(sample => sample.id || sample),
- "consequenceType",
+ "hgvs",
+ "samples",
+ "consequenceTypes",
"deleteriousness.SIFT",
"deleteriousness.polyphen",
"deleteriousness.revel",
@@ -79,136 +47,99 @@ export default class VariantUtils {
"conservation.phylop",
"conservation.phastCons",
"conservation.gerp",
- // AC / AF
- // fieldList (columns in the grid) is in the form: cohorts.RD38, cohorts.CG38
- // TSV in the form: cohort.RD38.alleleCount,cohort.RD38.altAlleleFreq
- ...studyIds.map(studyId => `cohorts.${studyId}`),
- // fieldList (columns in the grid) is in the form: popfreq.1kG_phase3, popfreq.GNOMAD_GENOMES
- // TSV in the form: popfreq.1kG_phase3_SAS,popfreq.GNOMAD_GENOMES_ALL,popfreq.GNOMAD_GENOMES_AFR
- ...popStudyIds,
+ "cohortStats.alt",
+ "populationFrequencies",
"clinicalInfo.clinvar",
"clinicalInfo.cosmic",
+ "acmgPrediction",
];
-
-
} else {
flatFieldList = fieldList
.filter(f => f.export && !f.excludeFromExport)
.flatMap(f => f.children?.filter(f => f.export && !f.excludeFromExport).map(x => f.id + "." + x.id) ?? f.id);
- // ESlint parse error. Cannot read property 'range' of null https://github.com/babel/babel-eslint/issues/681
- // flatFieldList = fieldList.filter(f => f.export).flatMap(f => f.children?.filter(f => f.export).map(x => `${f.id}.${x.id}`) ?? f.id);
}
- flatFieldList.forEach(f => {
- if ("id" === f) {
- headerString.push("id");
- headerString.push("SNP_ID");
- } else if (f.startsWith("cohorts.")) {
- // Cohorts Variant Browser
- studyIds.forEach(id => {
- if (f === "cohorts." + id) {
- headerString.push(`cohorts.${id}.alleleCount`, `cohorts.${id}.altAlleleFreq`);
- }
- });
- } else if ("frequencies.cohort" === f) {
- // Cohorts in Sample Variant Browser
- studyIds.forEach(id => headerString.push(`cohorts.${id}.alleleCount`, `cohorts.${id}.altAlleleFreq`));
- } else if (f.startsWith("popfreq.")) {
- // Pop freq in Variant Browser
- studiesPopFrequencies.forEach(study => {
- if (f === "popfreq." + study.id) {
- headerString.push(...study.populations.map(pop => "popfreq." + study.id + "_" + pop.id));
- }
- });
- } else if ("frequencies.populationFrequencies" === f) {
- // Pop freq in Sample Variant Browser
- studiesPopFrequencies.forEach(study => headerString.push(...study.populations.map(pop => "popfreq." + study.id + "_" + pop.id)));
- } else {
- headerString.push(f);
- }
-
- });
-
// TSV header
- rows.push(headerString.join("\t"));
-
- for (const v of variants) {
- const row = [];
- let genes = new Set();
- let ct = new Set();
- let sift, polyphen;
- let cadd = "-";
- let phylop = "-";
- let phastCons = "-";
- let gerp = "-";
- // cohorts
- // popfreqs
+ rows.push(flatFieldList.join("\t"));
+
+ for (const variant of variants) {
+ const genes = new Set();
+ const consequenceTypeNames = new Set();
+ const proteinSubstitutionScores = {sift: "", polyphen: "", revel: ""};
+ let cadd = "";
+ let phylop = "";
+ let phastCons = "";
+ let gerp = "";
let clinvar = new Set();
let cosmic = new Map();
- let prediction = "-";
+ let acmgPrediction = "";
populationMap = {};
const dataToTsv = {};
- const description = {sift: "-", polyphen: "-"};
- let min = 10;
- let max = 0;
- if (typeof v.annotation !== "undefined") {
- if (typeof v.annotation.consequenceTypes !== "undefined" && v.annotation.consequenceTypes.length > 0) {
- for (let j = 0; j < v.annotation.consequenceTypes.length; j++) {
- const cT = v.annotation.consequenceTypes[j];
- // gene
- if (typeof cT?.geneName === "string" && ct?.geneName !== "") {
- genes.add(cT.geneName);
+ if (variant.annotation) {
+ // Process the information in the ConsequenceType arrays
+ if (variant.annotation.consequenceTypes?.length > 0) {
+ for (const consequenceType of variant.annotation.consequenceTypes) {
+ // Genes
+ if (typeof consequenceType?.geneName === "string" && consequenceTypeNames?.geneName !== "") {
+ genes.add(consequenceType.geneName);
}
- // Consequence Type
- for (let z = 0; z < cT.sequenceOntologyTerms.length; z++) {
- const consequenceTypeName = cT.sequenceOntologyTerms[z].name;
- if (consequenceTypeName !== "") {
- ct.add(consequenceTypeName);
+ // Consequence Types
+ for (const consequenceTypeName of consequenceType.sequenceOntologyTerms) {
+ if (consequenceTypeName.name) {
+ let ct = consequenceTypeName.name;
+ if (consequenceType.geneName) {
+ ct += "(" + consequenceType.geneName + ")";
+ }
+ consequenceTypeNames.add(ct);
}
}
- // Sift, Polyphen
- if (typeof cT.proteinVariantAnnotation !== "undefined" &&
- typeof cT.proteinVariantAnnotation.substitutionScores !== "undefined") {
- for (let ss = 0; ss < cT.proteinVariantAnnotation.substitutionScores.length; ss++) {
- const substitutionScore = cT.proteinVariantAnnotation.substitutionScores[ss];
- const source = substitutionScore.source;
- switch (source) {
+ // Sift, Polyphen, Revel
+ if (consequenceType.proteinVariantAnnotation?.substitutionScores) {
+ let siftMin = 10;
+ let polyphenMax = 0;
+ let revelMax = 0;
+ for (const substitutionScore of consequenceType.proteinVariantAnnotation.substitutionScores) {
+ switch (substitutionScore.source) {
case "sift":
- if (substitutionScore.score < min) {
- min = substitutionScore.score;
- description.sift = substitutionScore.description + " (" + substitutionScore.score + ")";
+ if (substitutionScore.score < siftMin) {
+ siftMin = substitutionScore.score;
+ proteinSubstitutionScores.sift = substitutionScore.description + " (" + substitutionScore.score + ")";
}
break;
case "polyphen":
- if (substitutionScore.score >= max) {
- max = substitutionScore.score;
- description.polyphen = substitutionScore.description + " (" + substitutionScore.score + ")";
+ if (substitutionScore.score >= polyphenMax) {
+ polyphenMax = substitutionScore.score;
+ proteinSubstitutionScores.polyphen = substitutionScore.description + " (" + substitutionScore.score + ")";
+ }
+ break;
+ case "revel":
+ if (substitutionScore.score >= revelMax) {
+ revelMax = substitutionScore.score;
+ proteinSubstitutionScores.revel = substitutionScore.score;
}
break;
}
}
}
-
}
}
// CADD
- if (v.annotation?.functionalScore) {
- for (let fs = 0; fs < v.annotation.functionalScore.length; fs++) {
- if (v.annotation.functionalScore[fs] && v.annotation.functionalScore[fs].source === "cadd_scaled") {
- cadd = Number(v.annotation.functionalScore[fs].score).toFixed(2);
+ if (variant.annotation?.functionalScore) {
+ for (let fs = 0; fs < variant.annotation.functionalScore.length; fs++) {
+ if (variant.annotation.functionalScore[fs]?.source === "cadd_scaled") {
+ cadd = Number(variant.annotation.functionalScore[fs].score).toFixed(2);
}
}
}
// Conservation
- if (v.annotation?.conservation) {
- for (let cons = 0; cons < v.annotation.conservation.length; cons++) {
- const conservation = v.annotation.conservation[cons];
+ if (variant.annotation?.conservation) {
+ for (const conservation of variant.annotation.conservation) {
switch (conservation.source) {
case "phylop":
phylop = Number(conservation.score).toFixed(3);
@@ -227,19 +158,20 @@ export default class VariantUtils {
const populations = [];
const populationStudyBidimensional = [];
const populationMapExists = [];
- studiesPopFrequencies.forEach(study => {
+ populationFrequenciesStudies.forEach(study => {
populations[study.id] = study.populations.map(pop => pop.id);
study.populations.forEach(pop => {
populationMapExists[pop.id] = true;
});
populationStudyBidimensional[study.id] = populationMapExists;
});
- if (typeof studiesPopFrequencies !== "undefined" && studiesPopFrequencies.length > 0) {
- for (let j = 0; j < studiesPopFrequencies.length; j++) {
- const study = studiesPopFrequencies[j];
- for (const popFreqIdx in v.annotation.populationFrequencies) {
- if (Object.prototype.hasOwnProperty.call(v.annotation.populationFrequencies, popFreqIdx)) {
- const popFreq = v.annotation.populationFrequencies[popFreqIdx];
+
+ if (populationFrequenciesStudies?.length > 0) {
+ for (let j = 0; j < populationFrequenciesStudies.length; j++) {
+ const study = populationFrequenciesStudies[j];
+ for (const popFreqIdx in variant.annotation.populationFrequencies) {
+ if (Object.prototype.hasOwnProperty.call(variant.annotation.populationFrequencies, popFreqIdx)) {
+ const popFreq = variant.annotation.populationFrequencies[popFreqIdx];
if (UtilsNew.isNotUndefinedOrNull(popFreq)) {
const population = popFreq.population;
if (study.id === popFreq.study && populationStudyBidimensional[study.id][population] === true) {
@@ -251,18 +183,18 @@ export default class VariantUtils {
}
}
- if (v.annotation?.populationFrequencies?.length) {
- for (let pf = 0; pf < v.annotation.populationFrequencies.length; pf++) {
- const pop = v.annotation.populationFrequencies[pf].study + "_" + v.annotation.populationFrequencies[pf].population;
+ if (variant.annotation?.populationFrequencies?.length) {
+ for (let pf = 0; pf < variant.annotation.populationFrequencies.length; pf++) {
+ const pop = variant.annotation.populationFrequencies[pf].study + "_" + variant.annotation.populationFrequencies[pf].population;
if (typeof populationMap[pop] !== "undefined" && populationMap[pop] === "NA") {
- populationMap[pop] = Number(v.annotation.populationFrequencies[pf].altAlleleFreq).toFixed(4);
+ populationMap[pop] = Number(variant.annotation.populationFrequencies[pf].altAlleleFreq).toFixed(4);
}
}
}
- // Clinvar, cosmic
- if (v.annotation?.traitAssociation?.length) {
- v.annotation.traitAssociation.forEach(clinicalData => {
+ // Clinvar, Cosmic
+ if (variant.annotation?.traitAssociation?.length) {
+ variant.annotation.traitAssociation.forEach(clinicalData => {
if (clinicalData.source.name === "clinvar") {
// Verify isn't undefined
const clinicalSignificance = clinicalData?.variantClassification?.clinicalSignificance ? ` (${clinicalData?.variantClassification?.clinicalSignificance})`: "";
@@ -279,137 +211,129 @@ export default class VariantUtils {
});
}
- genes = genes.size > 0 ? [...genes].join(",") : "-";
- ct = ct.size > 0 ? [...ct].join(",") : "-";
- sift = typeof description.sift !== "undefined" ? description.sift : "-";
- polyphen = typeof description.polyphen !== "undefined" ? description.polyphen : "-";
- clinvar = clinvar.size > 0 ? [...clinvar].join(",") : "-";
- cosmic = cosmic.size > 0 ? [...cosmic.entries()].map(([traitId, histologies]) => traitId + "(" + [...histologies].join(",") + ")").join(",") : "-";
+ clinvar = clinvar.size > 0 ? [...clinvar].join(",") : "";
+ cosmic = cosmic.size > 0 ? [...cosmic.entries()].map(([traitId, histologies]) => traitId + "(" + [...histologies].join(",") + ")").join(",") : "";
}
// prediction
- if (v.evidences) {
- prediction = this.getClassificationByClinicalSignificance(v);
+ if (variant.evidences) {
+ acmgPrediction = this.getClassificationByClinicalSignificance(variant);
}
- // ID
+
+ // START PREPARING THE LINE
if (flatFieldList.includes("id")) {
- dataToTsv["id"] = v.chromosome + ":" + v.start + " " + v.reference + "/" + v.alternate;
+ dataToTsv["id"] = variant.chromosome + ":" + variant.start + ":" + (variant.reference || "-") + (":" + variant.alternate || "-");
+ }
+ if (flatFieldList.includes("snpId")) {
// SNP ID
- if (v?.id?.startsWith("rs")) {
- dataToTsv["SNP_ID"] = v.id;
- } else if (typeof v.annotation !== "undefined" && typeof v.annotation.xrefs !== "undefined" && v.annotation.xrefs.length > 0) {
- const annotation = v.annotation.xrefs.find(el => el.source === "dbSNP");
- if (typeof annotation !== "undefined") {
- dataToTsv["SNP_ID"] = annotation.id;
+ const dbSnpId = variant.names
+ ?.filter(name => name.startsWith("rs"))
+ ?.map(name => name)
+ .join(",");
+
+ if (dbSnpId) {
+ dataToTsv["snpId"] = dbSnpId;
+ } else {
+ if (variant.annotation?.xrefs?.length > 0) {
+ const dbSnpXref = variant.annotation.xrefs.find(el => el.source === "dbSNP");
+ if (dbSnpXref) {
+ dataToTsv["snpId"] = dbSnpXref.id;
+ } else {
+ dataToTsv["snpId"] = "";
+ }
} else {
- dataToTsv["SNP_ID"] = "-";
+ dataToTsv["snpId"] = "";
}
- } else {
- dataToTsv["SNP_ID"] = "-";
}
}
- // Genes
if (flatFieldList.includes("gene")) {
- dataToTsv["gene"] = genes;
+ dataToTsv["gene"] = genes.size > 0 ? [...genes].join(",") : "";
}
- // type
if (flatFieldList.includes("type")) {
- dataToTsv["type"] = v.type;
+ dataToTsv["type"] = variant.type;
}
- // consequence type
- if (flatFieldList.includes("consequenceType")) {
- dataToTsv["consequenceType"] = ct;
+ if (flatFieldList.includes("hgvs")) {
+ dataToTsv["hgvs"] = this.gethgvsValues(variant);
}
+ // Sample
if (samples?.length > 0) {
- const gtSamples = this.getGenotypeSamples(v, samples, nucleotideGenotype);
+ const gtSamples = this.getGenotypeSamples(variant, samples, nucleotideGenotype);
+ const sampleGenotypes = [];
gtSamples.forEach(sample => {
Object.keys(sample).forEach(sampleId => {
- if (flatFieldList.includes("sampleGenotypes." + sampleId)) {
- dataToTsv["sampleGenotypes."+ sampleId] = sample[sampleId];
- }
-
- if (flatFieldList.includes("samples." + sampleId)) {
- dataToTsv["samples."+ sampleId] = sample[sampleId];
+ if (sample[sampleId] !== "-") {
+ sampleGenotypes.push(sampleId + ":" + sample[sampleId]);
}
});
});
+ dataToTsv["samples"] = sampleGenotypes.join(",");
+ }
+
+ if (flatFieldList.includes("consequenceTypes")) {
+ dataToTsv["consequenceTypes"] = consequenceTypeNames.size > 0 ? [...consequenceTypeNames].join(",") : "";
}
- // deleteriousness
if (flatFieldList.includes("deleteriousness.SIFT")) {
- dataToTsv["deleteriousness.SIFT"] = sift;
+ dataToTsv["deleteriousness.SIFT"] = proteinSubstitutionScores.sift || "";
}
+
if (flatFieldList.includes("deleteriousness.polyphen")) {
- dataToTsv["deleteriousness.polyphen"] = polyphen;
+ dataToTsv["deleteriousness.polyphen"] = proteinSubstitutionScores.polyphen || "";
}
+
if (flatFieldList.includes("deleteriousness.revel")) {
- row.push("-"); // TODO deleteriousness Revel is missing
- dataToTsv["deleteriousness.revel"] = "-";
+ dataToTsv["deleteriousness.revel"] = proteinSubstitutionScores.revel || "";
}
+
if (flatFieldList.includes("deleteriousness.cadd")) {
dataToTsv["deleteriousness.cadd"] = cadd;
}
+
+ if (flatFieldList.includes("deleteriousness.spliceai")) {
+ dataToTsv["deleteriousness.spliceai"] = this.getSpliceAI(variant);
+ }
+
if (flatFieldList.includes("conservation.phylop")) {
dataToTsv["conservation.phylop"] = phylop;
}
+
if (flatFieldList.includes("conservation.phastCons")) {
dataToTsv["conservation.phastCons"] = phastCons;
}
+
if (flatFieldList.includes("conservation.gerp")) {
dataToTsv["conservation.gerp"] = gerp;
}
- if (flatFieldList.includes("deleteriousness.spliceai")) {
- dataToTsv["deleteriousness.spliceai"] = this.getSpliceAI(v);
- }
-
- if (flatFieldList.includes("hgvs")) {
- dataToTsv["hgvs"] = this.gethgvsValues(v);
- }
- // Allele stats (VB)
- // frequencies.cohort (SVB)
- // alleleStats.forEach(study => {
-
- // if (flatFieldList.includes(`cohorts.${study.id}`) || flatFieldList.includes("frequencies.cohort")) {
- // const ac = [];
- // const af = [];
- // study.stats.map(cohort => {
- // ac.push(`${cohort.cohortId}:${cohort.alleleCount}`);
- // af.push(`${cohort.cohortId}:${cohort.altAlleleFreq}`);
- // });
- // dataToTsv[`cohorts.${study.id}.alleleCount`] = ac.join(";");
- // dataToTsv[`cohorts.${study.id}.altAlleleFreq`] = af.join(";");
- // }
- // });
-
- v?.studies.forEach(study => {
- const studyId = study.studyId.split(":")[1];
- if (flatFieldList.includes(`cohorts.${studyId}`) || flatFieldList.includes("frequencies.cohort")) {
- const ac = [];
- const af = [];
- study?.stats.map(cohort => {
- ac.push(`${cohort.cohortId}:${cohort.alleleCount}`);
- af.push(`${cohort.cohortId}:${cohort.altAlleleFreq}`);
- });
- dataToTsv[`cohorts.${studyId}.alleleCount`] = ac.join(";");
- dataToTsv[`cohorts.${studyId}.altAlleleFreq`] = af.join(";");
+ if (flatFieldList.includes("cohortStats.alt")) {
+ const cohortStats = [];
+ for (const study of variant.studies) {
+ const studyId = study.studyId.split(":")[1];
+ for (const stats of study.stats) {
+ cohortStats.push(studyId + ":" + stats.cohortId + "=" + stats.altAlleleFreq);
+ }
}
- });
+ dataToTsv["cohortStats.alt"] = cohortStats.join(",");
+ }
- studiesPopFrequencies.forEach(study => {
- study.populations.forEach(pop => {
- if (flatFieldList.includes("popfreq." + study.id) || flatFieldList.includes("frequencies.populationFrequencies")) {
+ if (flatFieldList.includes("populationFrequencies")) {
+ const populationFrequencies = [];
+ for (const study of populationFrequenciesStudies) {
+ for (const pop of study.populations) {
const valuePopFreq = populationMap[study.id + "_" + pop.id];
- dataToTsv[`popfreq.${study.id}_${pop.id}`] = UtilsNew.isNotEmpty(valuePopFreq) ? valuePopFreq : "-";
+ if (valuePopFreq) {
+ populationFrequencies.push(study.id + ":" + pop.id + "=" + valuePopFreq);
+ }
}
- });
- });
+ }
+ dataToTsv["populationFrequencies"] = populationFrequencies.join(",");
+ }
if (flatFieldList.includes("clinicalInfo.clinvar")) {
dataToTsv["clinicalInfo.clinvar"] = clinvar;
@@ -420,12 +344,12 @@ export default class VariantUtils {
}
if (flatFieldList.includes("interpretation.prediction")) {
- dataToTsv["interpretation.prediction"] = prediction;
+ dataToTsv["acmgPrediction"] = acmgPrediction;
}
- const rowValues = headerString.map(head => dataToTsv[head]);
+
+ const rowValues = flatFieldList.map(header => dataToTsv[header]);
rows.push(rowValues.join("\t"));
}
-
return rows;
}
@@ -539,7 +463,6 @@ export default class VariantUtils {
}
static gethgvsValues(variant) {
-
BioinfoUtils.sort(variant.annotation?.consequenceTypes, v => v.geneName);
const gridConfig = {
geneSet: {
@@ -565,10 +488,15 @@ export default class VariantUtils {
const results = [];
for (const index of showArrayIndexes) {
const consequenceType = variant.annotation.consequenceTypes[index];
+
const hgvsTranscriptIndex = variant.annotation.hgvs.findIndex(hgvs => hgvs.startsWith(consequenceType.transcriptId));
+ if (hgvsTranscriptIndex > -1) {
+ results.push(`${this.getHgvs(consequenceType.transcriptId, variant.annotation.hgvs) || ""}`);
+ }
+
const hgvsProteingIndex = variant.annotation.hgvs.findIndex(hgvs => hgvs.startsWith(consequenceType.proteinVariantAnnotation?.proteinId));
- if (hgvsTranscriptIndex > -1 || hgvsProteingIndex > -1) {
- results.push(`${this.getHgvs(consequenceType.transcriptId, variant.annotation.hgvs) || "-"} ${this.getHgvs(consequenceType.proteinVariantAnnotation?.proteinId, variant.annotation.hgvs) || "-"}`);
+ if (hgvsProteingIndex > -1) {
+ results.push(`${this.getHgvs(consequenceType.proteinVariantAnnotation?.proteinId, variant.annotation.hgvs) || ""}`);
}
}
return results.join();
@@ -612,21 +540,7 @@ export default class VariantUtils {
}
return dscore;
}
- return "-";
- }
-
- static removeUnlockQuery(lockedFields, preparedQuery, executedQuery) {
- // Get all keys
- const queryKeys = new Set([...Object.keys(preparedQuery), ...Object.keys(executedQuery)]);
-
- // Remove keys belong to lockedFields
- lockedFields.forEach(key => queryKeys.delete(key.id));
-
- // Remove all key not belong to lockedFields
- queryKeys.forEach(key => {
- delete preparedQuery[key];
- delete executedQuery[key];
- });
+ return "";
}
static validateQuery(query) {