for for insertion rendering in Gingr

marbl · Sep 30, 2016 · ce55be5 · ce55be5
1 parent 748759a
commit ce55be5
Showing 1 changed file with 8 additions and 1 deletion.
diff --git a/src/harvest/VariantList.cpp b/src/harvest/VariantList.cpp
@@ -274,7 +274,14 @@ void VariantList::addVariantsFromAlignment(const vector<string> & seqs, const Re
 
 			if ( referenceList.getReferenceCount() )
 			{
-				varNew->reference = referenceList.getReference(sequence).sequence[position];
+				if ( offset > 0 )
+				{
+					varNew->reference = '-';
+				}
+				else
+				{
+					varNew->reference = referenceList.getReference(sequence).sequence[position];
+				}
 			}
 			else
 			{