From cd04bdd410f0c09d6bd286299e37b9e249ae4689 Mon Sep 17 00:00:00 2001
From: Luca Denti <ldenti92@gmail.com>
Date: Thu, 30 Apr 2020 18:24:11 +0200
Subject: [PATCH] Skip variants close to reference sequence ends

---
 var_block.hpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var_block.hpp b/var_block.hpp
index 5f8e719..ade4ab8 100644
--- 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;
       }