Changed the skalo command to be ska lo and added documentation for sk…

…alo to the main doc

src/cli.rs

@@ -358,7 +358,7 @@ pub enum Commands {
         #[arg(long, default_value_t = DEFAULT_STRAND)]
         single_strand: bool,
     },
-    Indel {
+    Lo {
         /// input SKA2 file
         #[arg(short = 'i', long, help_heading = "input")]
         input_skf: String,

src/lib.rs

@@ -336,6 +336,24 @@
 //! to use the same cutoff. Alternatively `ska cov` can be run on every sample
 //! independently (`gnu parallel` would be an efficient way to do this).
 //!
+//! ## ska lo
+//!
+//! Runs "skalo", a graph-based algorithm for inferring variants from WGS outbreak data.
+//! Skalo takes as input a `.skf` file generated by the `ska build` command.
+//!
+//! To run skalo on a file named `my_file.skf` use the following command `ska lo -i my_file.skf`.
+//!
+//! The skalo method
+//! can be modified using the following flags:
+//! * `-i` the path to the `.skf` file to be analysed
+//! * `-r` the path to a reference genome that the detected SNPs can be mapped onto
+//! * `-o` the prefix for the path of the output files
+//! * `-m` the maximum fraction of missing data permissible for a site where a possible SNP has been detected (default = 0.2)
+//! * `-d` the depth of the recursive path allowed during graph traversal (default = 4)
+//! * `-n` maximum number of internal indel k-mers (default = 2)
+//! * `-t` number of threads to use for parallel computation (default = 1)
+//!
+//!
 //! # API usage
 //!
 //! See the submodule documentation linked below.
@@ -786,7 +804,7 @@ pub fn main() {
             }
             eprintln!("Estimated cutoff\t{cutoff}");
         }
-        Commands::Indel {
+        Commands::Lo {
             input_skf,
             reference,
             output,