fix: lint and update version

Author: Ebedthan

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name    = "sabreur"
-version = "0.5.0"
+version = "0.6.0"
 authors = ["Anicet Ebou <anicet.ebou@gmail.com>"]
 edition = "2018"
 exclude     = ["CODE_OF_CONDUCT.md", "tests/*", "benches/*", ".github/*", ".cargo/*"]

Cargo.toml

@@ -47,8 +47,8 @@ pub fn se_demux<'a>(
         // let iter = my_vec.iter() to further stop
         // the find at first match.
         let mut iter = my_vec.iter();
-        let matched_barcode = iter
-            .find(|&&x| bc_cmp(x, &record.seq().as_ref()[..bc_len], mismatch));
+        let matched_barcode =
+            iter.find(|&&x| bc_cmp(x, &record.seq().as_ref()[..bc_len], mismatch));
 
         if let Some(i) = matched_barcode {
             nb_records.entry(i).and_modify(|e| *e += 1).or_insert(1);
@@ -89,11 +89,9 @@ pub fn pe_demux<'a>(
     let (reverse_reader, _compression) = niffler::send::from_path(reverse)?;
 
     // Get records
-    let mut forward_fastx_reader =
-        needletail::parse_fastx_reader(forward_reader)?;
+    let mut forward_fastx_reader = needletail::parse_fastx_reader(forward_reader)?;
     //forward_records = forward_records.records();
-    let mut reverse_fastx_reader =
-        needletail::parse_fastx_reader(reverse_reader)?;
+    let mut reverse_fastx_reader = needletail::parse_fastx_reader(reverse_reader)?;
 
     // Clone barcode values in barcode_data structure for future iteration
     let my_vec = barcode_data.keys().cloned().collect::<Vec<_>>();
@@ -114,8 +112,7 @@ pub fn pe_demux<'a>(
     while let Some(r) = forward_fastx_reader.next() {
         let record = r.expect("invalid record");
         let mut iter = my_vec.iter();
-        let matched_barcode =
-            iter.find(|&&x| bc_cmp(x, &record.seq()[..bc_len], mismatch));
+        let matched_barcode = iter.find(|&&x| bc_cmp(x, &record.seq()[..bc_len], mismatch));
 
         if let Some(i) = matched_barcode {
             nb_records.entry(i).and_modify(|e| *e += 1).or_insert(1);
@@ -141,8 +138,7 @@ pub fn pe_demux<'a>(
     while let Some(r) = reverse_fastx_reader.next() {
         let record = r.expect("invalid record");
         let mut iter = my_vec.iter();
-        let matched_barcode =
-            iter.find(|&&x| bc_cmp(x, &record.seq()[..bc_len], mismatch));
+        let matched_barcode = iter.find(|&&x| bc_cmp(x, &record.seq()[..bc_len], mismatch));
 
         if let Some(i) = matched_barcode {
             nb_records.entry(i).and_modify(|e| *e += 1).or_insert(1);

src/demux.rs

@@ -48,12 +48,8 @@ fn main() -> anyhow::Result<()> {
     // add option to change compression of output
     let mut format = niffler::send::compression::Format::No;
     if matches.contains_id("format") {
-        format = utils::to_niffler_format(
-            matches.get_one::<String>("format").unwrap(),
-        )
-        .with_context(|| {
-            anyhow!("Could not convert compression format to niffler format")
-        })?;
+        format = utils::to_niffler_format(matches.get_one::<String>("format").unwrap())
+            .with_context(|| anyhow!("Could not convert compression format to niffler format"))?;
     }
 
     let raw_level: u8 = *matches.get_one("level").unwrap();
@@ -78,12 +74,25 @@ fn main() -> anyhow::Result<()> {
     // Handle output dir
     let outdir_exists = output.exists();
     if outdir_exists && !force {
-        error!("output folder '{}', already exists! change it using --out or use --force", output.display());
+        error!(
+            "output folder '{}', already exists! change it using --out or use --force",
+            output.display()
+        );
         process::exit(exitcode::CANTCREAT);
     } else if outdir_exists && force {
         info!("Reusing directory {}", output.display());
-        fs::remove_dir_all(output).with_context(|| anyhow!("Could not remove folder '{}'. Do you have permission to remove this folder?", output.display()))?;
-        fs::create_dir(output).with_context(|| anyhow!("Could not create folder '{}'. Do you have permission to create this folder?", output.display()))?;
+        fs::remove_dir_all(output).with_context(|| {
+            anyhow!(
+                "Could not remove folder '{}'. Do you have permission to remove this folder?",
+                output.display()
+            )
+        })?;
+        fs::create_dir(output).with_context(|| {
+            anyhow!(
+                "Could not create folder '{}'. Do you have permission to create this folder?",
+                output.display()
+            )
+        })?;
     } else if !outdir_exists {
         fs::create_dir(output)?;
     }

src/main.rs

@@ -62,9 +62,7 @@ pub fn create_relpath_from(basedir: &mut PathBuf, input: Vec<&str>) -> PathBuf {
 }
 
 // to_niffler_format function
-pub fn to_niffler_format(
-    format: &str,
-) -> anyhow::Result<niffler::send::compression::Format> {
+pub fn to_niffler_format(format: &str) -> anyhow::Result<niffler::send::compression::Format> {
     match format {
         "gz" => Ok(niffler::send::compression::Format::Gzip),
         "bz2" => Ok(niffler::send::compression::Format::Bzip),
@@ -75,9 +73,7 @@ pub fn to_niffler_format(
 }
 
 // Convert niffler compression format to a file extension
-pub fn to_compression_ext(
-    compression: niffler::send::compression::Format,
-) -> String {
+pub fn to_compression_ext(compression: niffler::send::compression::Format) -> String {
     match compression {
         niffler::send::compression::Format::Gzip => ".gz".to_string(),
         niffler::send::compression::Format::Bzip => ".bz2".to_string(),
@@ -143,8 +139,7 @@ pub fn write_seqs<'a>(
     record: &'a needletail::parser::SequenceRecord,
     level: niffler::Level,
 ) -> anyhow::Result<()> {
-    let mut handle =
-        niffler::send::get_writer(Box::new(file), compression, level)?;
+    let mut handle = niffler::send::get_writer(Box::new(file), compression, level)?;
 
     match record.format() {
         needletail::parser::Format::Fasta => needletail::parser::write_fasta(
@@ -173,10 +168,7 @@ mod tests {
     #[test]
     fn test_create_relpath_from() {
         assert_eq!(
-            create_relpath_from(
-                &mut PathBuf::from("path"),
-                ["to", "file"].to_vec()
-            ),
+            create_relpath_from(&mut PathBuf::from("path"), ["to", "file"].to_vec()),
             PathBuf::from("path/to/file")
         );
     }