Add gap scoring function to header

kaplannp · Nov 3, 2022 · 04ccbf7 · 04ccbf7
1 parent 00b0ae4
commit 04ccbf7
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/src/aligner.hpp b/src/aligner.hpp
@@ -35,6 +35,9 @@ namespace vg {
     static constexpr int8_t default_gap_extension = 1;
     static constexpr int8_t default_full_length_bonus = 5;
     static constexpr double default_gc_content = 0.5;
+
+    /// Score a gap with the given open and extension scores.
+    int32_t score_gap(size_t gap_length, int32_t gap_open, int32_t gap_extension);
 
     /**
      * The abstract interface that any Aligner should implement.