gff -- show gene types IFF they are not associated with visible trans…

…cripts. Previous implementation never showed gene types.
igvteam · Aug 16, 2020 · a2a7331 · a2a7331
1 parent d032bf4
commit a2a7331
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/js/feature/featureSource.js b/js/feature/featureSource.js
@@ -56,7 +56,7 @@ class FeatureSource {
 
         // Default GFF filter -- these feature types will be filtered out
         if (undefined === config.filterTypes) {
-            config.filterTypes = ['chromosome', 'gene']
+            config.filterTypes = ['chromosome']
         }
 
         if (config.features && Array.isArray(config.features)) {

diff --git a/js/feature/gffHelper.js b/js/feature/gffHelper.js
@@ -218,11 +218,17 @@ class GFFHelper {
                     transcripts[transcriptId] = gffTranscript;
                     combinedFeatures.push(gffTranscript);
                     consumedFeatures.add(f);
-                    gffTranscript.gene = geneMap[f.parent];
+                    const g = geneMap[f.parent];
+                    if(g) {
+                        gffTranscript.gene = geneMap[f.parent];
+                        consumedFeatures.add(g);
+                    }
                 }
             }
         }
 
+        // Remove assigned genes
+
         // Add exons
         for (let f of features) {
             if (exonTypes.has(f.type)) {