change default mapper to strobealign

wwood · May 31, 2024 · f6d57fe · f6d57fe
1 parent 7dae171
commit f6d57fe
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/src/cli.rs b/src/cli.rs
@@ -21,7 +21,7 @@ const MAPPING_SOFTWARE_LIST: &[&str] = &[
  "minimap2-no-preset",
  "strobealign",
 ];
-const DEFAULT_MAPPING_SOFTWARE: &str = "minimap2-sr";
+const DEFAULT_MAPPING_SOFTWARE: &str = "strobealign";
 
 lazy_static! {
  pub static ref COVERM_CLUSTER_COMMAND_DEFINITION: GalahClustererCommandDefinition = {
@@ -50,13 +50,9 @@ fn add_mapping_options(manual: Manual) -> Manual {
  Section::new("Mapping algorithm options")
  .option(Opt::new("NAME").short("-p").long("--mapper").help(&format!(
  "Underlying mapping software used {}. One of: {}",
- default_roff("minimap2-sr"),
+ default_roff("strobealign"),
  bird_tool_utils::clap_utils::table_roff(&[
  &["name", "description"],
- &[
- &monospace_roff("minimap2-sr"),
- &format!("minimap2 with '{}' option", &monospace_roff("-x sr"))
- ],
  &[
  &monospace_roff("strobealign"),
  "strobealign using default parameters"
@@ -69,6 +65,10 @@ fn add_mapping_options(manual: Manual) -> Manual {
  &monospace_roff("bwa-mem2"),
  "bwa-mem2 using default parameters"
  ],
+ &[
+ &monospace_roff("minimap2-sr"),
+ &format!("minimap2 with '{}' option", &monospace_roff("-x sr"))
+ ],
  &[
  &monospace_roff("minimap2-ont"),
  &format!("minimap2 with '{}' option", &monospace_roff("-x map-ont"))