From 108953c611409ce47ef8b22c21a7854d10ca0fbd Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 13 Jun 2019 15:58:57 +0100
Subject: [PATCH] JAL-3303 ignore deletions when computing peptide variants

---
 src/jalview/datamodel/MappedFeatures.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 25f5ba4..4c63916 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -144,7 +144,7 @@ public class MappedFeatures
       for (String allele : alleles)
       {
         allele = allele.trim().toUpperCase();
-        if (allele.length() > 1)
+        if (allele.length() > 1 || "-".equals(allele))
         {
           continue; // multi-locus variant
         }
-- 
1.7.10.2