Io::is_gzip_path

.gitignore

@@ -1,2 +1,4 @@
 /target
 .vscode
+*.fq
+*.fq.gz

Cargo.toml

@@ -2,7 +2,8 @@
 authors = [
     "Nathan Roach <[email protected]>",
     "Tim Fennell <[email protected]>",
-    "Nils Homer <[email protected]>"
+    "Nils Homer <[email protected]>",
+    "Brent Pedersen <[email protected]>"
 ]
 name = "fqtk"
 version = "0.3.1-rc.1"
@@ -36,7 +37,7 @@ bstr = "1.0.1"
 clap = { version = "4.3.22", features = ["derive"] }
 enum_dispatch = "0.3.8"
 env_logger = "0.9.3"
-fgoxide = "0.3.0"
+fgoxide = { git = "https://github.com/brentp/fgoxide", branch = "pub-is-gz" }
 flate2 = { version = "1.0.25", features = ["zlib-ng"] }  # Force the faster backend that requires a C compiler
 itertools = "0.10.5"
 log = "0.4.17"

src/bin/commands/trimmer.rs

@@ -109,11 +109,6 @@ fn create_writer<P: AsRef<Path>>(name: P) -> Result<BufWriter<File>, Error> {
     Ok(BufWriter::new(File::create(name)?))
 }
 
-fn check_extension(p: &Path) -> bool {
-    let ext = p.extension().map_or("", |v| v.to_str().unwrap_or(""));
-    ["bgz", "gz"].contains(&ext)
-}
-
 impl TrimmerOpts {
     fn prepare(&self) -> Result<(Pool, Vec<PooledWriter>, VecOfFqReaders), Error> {
         let fgio = Io::new(5, BUFFER_SIZE);
@@ -130,7 +125,7 @@ impl TrimmerOpts {
             .output
             .iter()
             .map(|p| {
-                if !check_extension(p) {
+                if !Io::is_gzip_path(p) {
                     log::warn!(
                         "Output file {} does not end with .gz or .bgz. Writing bgzipped output to {} instead.",
                         p.display(),
@@ -265,29 +260,3 @@ impl Command for TrimmerOpts {
         Ok(())
     }
 }
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use std::path::PathBuf;
-
-    #[test]
-    fn test_check_extension_gz() {
-        let path = PathBuf::from("test_file.gz");
-        assert_eq!(
-            check_extension(&path),
-            true,
-            "The function should return true for .gz extension"
-        );
-    }
-
-    #[test]
-    fn test_check_extension_txt() {
-        let path = PathBuf::from("test_file.txt");
-        assert_eq!(
-            check_extension(&path),
-            false,
-            "The function should return false for .txt extension"
-        );
-    }
-}