Adopt HiFi parameters that look competitive with minimap2 on the 10k …

…read set
vgteam · Jun 26, 2024 · ef2a138 · ef2a138 · adamnovak · Jun 27, 2024
1 parent c029ba2
commit ef2a138
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/subcommand/giraffe_main.cpp b/src/subcommand/giraffe_main.cpp
@@ -917,9 +917,9 @@ int main_giraffe(int argc, char** argv) {
         .add_entry<double>("max-indel-bases-per-base", 2.45)
         .add_entry<int>("item-bonus", 20)
         .add_entry<double>("item-scale", 1.0)
-        .add_entry<double>("gap-scale", 0.06759721757973396)
+        .add_entry<double>("gap-scale", 0.2)
         .add_entry<double>("chain-score-threshold", 100.0)
-        .add_entry<int>("min-chains", 2)
+        .add_entry<int>("min-chains", 4)
         .add_entry<double>("min-chain-score-per-base", 0.06)
         .add_entry<size_t>("max-chains-per-tree", 3)
         .add_entry<int>("max-min-chain-score", 100)