From 04ccbf74a11c265da2fcad8210165128bb4352d3 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Tue, 1 Nov 2022 19:02:37 -0400
Subject: [PATCH] Add gap scoring function to header
---
src/aligner.hpp | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/aligner.hpp b/src/aligner.hpp
index 628c9fdbeca..d4f5d5ed4ef 100644
--- 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.