Update Impact annotation to work properly on symbolic alleles (#288)

BimberLab · Oct 11, 2023 · 0d04d4e · 0d04d4e
1 parent 3b48e10
commit 0d04d4e
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/src/main/java/com/github/discvrseq/walkers/annotator/Impact.java b/src/main/java/com/github/discvrseq/walkers/annotator/Impact.java
@@ -56,15 +56,16 @@ public Map<String, Object> annotate(ReferenceContext ref, VariantContext vc, All
         Map<Allele, String> effectMap = new HashMap<>();
 
         for (Allele a : vc.getAlternateAlleles()) {
-            if (!annByAllele.containsKey(a.getBaseString())) {
+            // Note: use displayString to handle symbolic alleles
+            if (!annByAllele.containsKey(a.getDisplayString())) {
                 continue;
             }
 
             Set<String> impacts = new HashSet<>();
             Set<String> hig = new HashSet<>();
             Set<String> og = new HashSet<>();
             Set<String> effects = new HashSet<>();
-            for (String[] split : annByAllele.get(a.getBaseString())) {
+            for (String[] split : annByAllele.get(a.getDisplayString())) {
                 if (split.length > 7 && "protein_coding".equals(split[7])) {
                     impacts.add(split[2]);