Merge pull request #956 from opencb/TASK-6637

TASK-6637 - Add NA genotype to clinical interpreter genotype filter

src/sites/iva/conf/config.js

@@ -25,8 +25,8 @@ const hosts = [
         url: "https://demo.app.zettagenomics.com/opencga"
     },
     {
-        id: "reference",
-        url: "https://test.app.zettagenomics.com/reference/opencga"
+        id: "xeta-110e",
+        url: "https://test.app.zettagenomics.com/xeta-110e/opencga"
     },
 ];
 

src/webcomponents/commons/filters/sample-genotype-filter.js

@@ -62,14 +62,16 @@ export default class SampleGenotypeFilter extends LitElement {
         }
 
         if (changedProperties.has("config")) {
-            this._config = {...this.getDefaultConfig(), ...this.config};
+            this._config = {
+                ...this.getDefaultConfig(),
+                ...this.config,
+            };
         }
 
         super.update(changedProperties);
     }
 
     filterChange(e) {
-
         // Prepare sample query filter
         let sampleFilter = this.sampleId;
         if (e.detail.value) {
@@ -79,47 +81,50 @@ export default class SampleGenotypeFilter extends LitElement {
         LitUtils.dispatchCustomEvent(this, "filterChange", sampleFilter);
     }
 
+    render() {
+        const genotypes = this.genotypes ?? [];
+        return html`
+            <select-field-filter
+                .data="${this._config?.genotypes}"
+                .value=${genotypes}
+                .config="${{
+                    multiple: true,
+                    liveSearch: false
+                }}"
+                @filterChange="${this.filterChange}">
+            </select-field-filter>
+        `;
+    }
+
     getDefaultConfig() {
         // HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3)
         return {
             genotypes: [
                 {
-                    id: "0/1", name: "HET"
+                    id: "0/1", name: "Heterozygous (0/1)"
                 },
                 {
-                    id: "1/1", name: "HOM_ALT"
+                    id: "1/1", name: "Homozygous Alternate (1/1)"
                 },
                 {
                     separator: true
                 },
                 {
-                    id: "1/2", name: "BIALLELIC (1/2)"
+                    id: "1", name: "Haploid (1)"
+                },
+                {
+                    id: "1/2", name: "Biallelic (1/2)"
                 },
+                {
+                    id: "NA", name: "NA"
+                }
                 // {
                 //     id: "./.", name: "Missing"
                 // },
-                // {
-                //     id: "NA", name: "NA"
-                // }
             ]
         };
     }
 
-    render() {
-        const genotypes = this.genotypes ?? [];
-        return html`
-            <select-field-filter
-                .data="${this._config?.genotypes}"
-                .value=${genotypes}
-                .config="${{
-                    multiple: true,
-                    liveSearch: false
-                }}"
-                @filterChange="${this.filterChange}">
-            </select-field-filter>
-        `;
-    }
-
 }
 
 customElements.define("sample-genotype-filter", SampleGenotypeFilter);