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.