Merge pull request #55 from tmaklin/master

Add optional output filename option `-o` to `ska weed`.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ska"
-version = "0.3.2"
+version = "0.3.3"
 authors = [
     "John Lees <[email protected]>",
     "Simon Harris <[email protected]>",

src/cli.rs

@@ -268,6 +268,10 @@ pub enum Commands {
         /// A FASTA file containing sequences to remove
         weed_file: Option<String>,
 
+        /// Output filename (omit to overwrite input file)
+        #[arg(short)]
+        output: Option<String>,
+
         /// Remove k-mers not in the weed_file
         #[arg(long, default_value_t = false)]
         reverse: bool,

src/lib.rs

@@ -243,7 +243,8 @@
 //!
 //! Remove (weed) split k-mers from an `.skf` file. The split k-mers to be removed
 //! are generated from a FASTA file, which may for example contain known transposons or
-//! other repeat sequences. As with `delete`, the input `.skf` file is overwritten.
+//! other repeat sequences. As with `delete`, the input `.skf` file is overwritten by default.
+//! Use `-o` to write the results to a new file instead of overwriting the input `.skf`.
 //!
 //! ```bash
 //! ska weed all_samples.skf MGEs.fa
@@ -635,6 +636,7 @@ pub fn main() {
         Commands::Weed {
             skf_file,
             weed_file,
+            output,
             reverse,
             min_freq,
             ambig_mask,
@@ -649,7 +651,7 @@ pub fn main() {
                     *min_freq,
                     filter,
                     *ambig_mask,
-                    skf_file,
+                    if output.is_none() { skf_file } else { output.as_ref().unwrap().as_str() },
                 );
             } else if let Ok(mut ska_array) = MergeSkaArray::<u128>::load(skf_file) {
                 weed(
@@ -659,7 +661,7 @@ pub fn main() {
                     *min_freq,
                     filter,
                     *ambig_mask,
-                    skf_file,
+                    if output.is_none() { skf_file } else { output.as_ref().unwrap().as_str() },
                 );
             } else {
                 panic!("Could not read input file: {skf_file}");