Skip variants close to reference sequence ends

AlgoLab · Apr 30, 2020 · cd04bdd · cd04bdd
1 parent c8eb1a7
commit cd04bdd
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/var_block.hpp b/var_block.hpp
@@ -74,7 +74,11 @@ class VB {
 
       Variant *v = &variants[v_index];
 
-      if (!v->is_present) {
+      if (!v->is_present || v->ref_pos < k || v->ref_pos > (int)reference.size() - k) {
+	// Here we could use k/2 but with k the probability to not
+	// exceed the reference length due to insertions is
+	// higher. Anyway, it shouldn't be common to have variants
+	// near to reference ends
         kmers[v_index] = _kmers;
         continue;
       }