Get all elements inside intergenic variants

leexgh · Aug 26, 2024 · 8c7ecb8 · 8c7ecb8
1 parent 066ae91
commit 8c7ecb8
Showing 1 changed file with 11 additions and 8 deletions.
diff --git a/...ava/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java b/...ava/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java
@@ -4,6 +4,7 @@
 import org.cbioportal.genome_nexus.model.TranscriptConsequenceSummary;
 import org.cbioportal.genome_nexus.model.VariantAnnotationSummary;
 import org.cbioportal.genome_nexus.model.IntergenicConsequenceSummary;
+import org.cbioportal.genome_nexus.model.IntergenicConsequences;
 import org.cbioportal.genome_nexus.model.RevisedProteinEffectJsonRecord;
 import org.cbioportal.genome_nexus.model.TranscriptConsequence;
 import org.cbioportal.genome_nexus.model.VariantAnnotation;
@@ -115,14 +116,16 @@ public VariantAnnotationSummary getAnnotationSummaryForCanonical(VariantAnnotati
             if (canonicalTranscript == null && annotation.getIntergenicConsequences() != null && !annotation.getIntergenicConsequences().isEmpty()) {
                 // Set variantClassification to "IGR" and when variant is "intergenic_variant".
                 // This is useful for genome nexus annotation pipeline, so when doing curation, those mutations will be filtered out by "IGR" rule, instead of being imported as "MUTATED".
-                IntergenicConsequenceSummary intergenicConsequenceSummary = new IntergenicConsequenceSummary();
-                // Get related fields from annotation.getIntergenicConsequences() and add "variantClassification"
-                intergenicConsequenceSummary.setVariantClassification(this.variantClassificationResolver.resolve(annotation, canonicalTranscript));
-                // Use the first intergenic consequence to set impact, variantAllele and consequenceTerms
-                intergenicConsequenceSummary.setImpact(annotation.getIntergenicConsequences().get(0).getImpact());
-                intergenicConsequenceSummary.setVariantAllele(annotation.getIntergenicConsequences().get(0).getVariantAllele());
-                intergenicConsequenceSummary.setConsequenceTerms(annotation.getIntergenicConsequences().get(0).getConsequenceTerms());
-                annotationSummary.setIntergenicConsequenceSummaries(Collections.singletonList(intergenicConsequenceSummary));
+                List<IntergenicConsequenceSummary> intergenicConsequenceSummaries = new ArrayList<>();
+                for (IntergenicConsequences intergenicConsequence : annotation.getIntergenicConsequences()) {
+                    IntergenicConsequenceSummary intergenicConsequenceSummary = new IntergenicConsequenceSummary();
+                    intergenicConsequenceSummary.setVariantClassification(this.variantClassificationResolver.resolve(annotation, canonicalTranscript));
+                    intergenicConsequenceSummary.setImpact(intergenicConsequence.getImpact());
+                    intergenicConsequenceSummary.setVariantAllele(intergenicConsequence.getVariantAllele());
+                    intergenicConsequenceSummary.setConsequenceTerms(intergenicConsequence.getConsequenceTerms());
+                    intergenicConsequenceSummaries.add(intergenicConsequenceSummary);
+                }
+                annotationSummary.setIntergenicConsequenceSummaries(intergenicConsequenceSummaries);
             }
             else {
                 annotationSummary.setTranscriptConsequenceSummary(this.getTranscriptSummary(annotation, canonicalTranscript, vuesMap));