From bcd7ac9ed2fbc9f300ae415ae96138bbbd698a6a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tommi=20M=C3=A4klin?= <tommi@maklin.fi>
Date: Fri, 22 Sep 2023 16:04:56 +0300
Subject: [PATCH 1/2] Add optional output filename `-o` option to `ska weed`.

---
 src/cli.rs | 4 ++++
 src/lib.rs | 8 +++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/cli.rs b/src/cli.rs
index b598634..e004b7a 100644
--- a/src/cli.rs
+++ b/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,
diff --git a/src/lib.rs b/src/lib.rs
index 264cfda..de48c27 100644
--- a/src/lib.rs
+++ b/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}");

From 1a061afb42e04ad2f8f7fed47e6942409a52b873 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tommi=20M=C3=A4klin?= <tommi@maklin.fi>
Date: Mon, 25 Sep 2023 10:06:35 +0300
Subject: [PATCH 2/2] Bump version

---
 Cargo.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.toml b/Cargo.toml
index 7be10cf..24c93d8 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "ska"
-version = "0.3.2"
+version = "0.3.3"
 authors = [
     "John Lees <jlees@ebi.ac.uk>",
     "Simon Harris <simon.harris@gatesfoundation.org>",